1
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Reinhard M, Kunnus K, Ledbetter K, Biasin E, Zederkof DB, Alonso-Mori R, van Driel TB, Nelson S, Kozina M, Borkiewicz OJ, Lorenc M, Cammarata M, Collet E, Sokaras D, Cordones AA, Gaffney KJ. Observation of a Picosecond Light-Induced Spin Transition in Polymeric Nanorods. ACS NANO 2024; 18:15468-15476. [PMID: 38833689 DOI: 10.1021/acsnano.3c10042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Spin transition (ST) materials are attractive for developing photoswitchable devices, but their slow material transformations limit device applications. Size reduction could enable faster switching, but the photoinduced dynamics at the nanoscale remains poorly understood. Here, we report a femtosecond optical pump multimodal X-ray probe study of polymeric nanorods. Simultaneously tracking the ST order parameter with X-ray emission spectroscopy and structure with X-ray diffraction, we observe photodoping of the low-spin-lattice within ∼150 fs. Above a ∼16% photodoping threshold, the transition to the high-spin phase occurs following an incubation period assigned to vibrational energy redistribution within the nanorods activating the molecular spin switching. Above ∼60% photodoping, the incubation period disappears, and the transition completes within ∼50 ps, preceded by the elastic nanorod expansion in response to the photodoping. These results support the feasibility of ST material-based GHz optical switching applications.
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Affiliation(s)
- Marco Reinhard
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Kristjan Kunnus
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Kathryn Ledbetter
- Department of Physics, Stanford University, Stanford, California 94305, United States
| | - Elisa Biasin
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | | | - Roberto Alonso-Mori
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Tim Brandt van Driel
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Silke Nelson
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Michael Kozina
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Olaf J Borkiewicz
- X-ray Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Maciej Lorenc
- Univ Rennes, CNRS, IPR (Institut de Physique de Rennes)─UMR 6251, 35000 Rennes, France
| | - Marco Cammarata
- Univ Rennes, CNRS, IPR (Institut de Physique de Rennes)─UMR 6251, 35000 Rennes, France
| | - Eric Collet
- Univ Rennes, CNRS, IPR (Institut de Physique de Rennes)─UMR 6251, 35000 Rennes, France
| | - Dimosthenis Sokaras
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Amy A Cordones
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Kelly J Gaffney
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
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2
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Powers-Riggs NE, Birgisson BO, Raj SL, Biasin E, Lenzen P, Zederkof DB, Haubro M, Tveiten DKV, Hartsock RW, van Driel TB, Kunnus K, Chollet M, Robinson JS, Nelson S, Forbes R, Haldrup K, Pedersen KS, Levi G, Ougaard Dohn A, Jónsson H, Mo Ller KB, Natan A, Nielsen MM, Gaffney KJ. Characterization of Deformational Isomerization Potential and Interconversion Dynamics with Ultrafast X-ray Solution Scattering. J Am Chem Soc 2024; 146:13962-13973. [PMID: 38727611 DOI: 10.1021/jacs.4c00817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Dimeric complexes composed of d8 square planar metal centers and rigid bridging ligands provide model systems to understand the interplay between attractive dispersion forces and steric strain in order to assist the development of reliable methods to model metal dimer complexes more broadly. [Ir2 (dimen)4]2+ (dimen = para-diisocyanomenthane) presents a unique case study for such phenomena, as distortions of the optimal structure of a ligand with limited conformational flexibility counteract the attractive dispersive forces from the metal and ligand to yield a complex with two ground state deformational isomers. Here, we use ultrafast X-ray solution scattering (XSS) and optical transient absorption spectroscopy (OTAS) to reveal the nature of the equilibrium distribution and the exchange rate between the deformational isomers. The two ground state isomers have spectrally distinct electronic excitations that enable the selective excitation of one isomer or the other using a femtosecond duration pulse of visible light. We then track the dynamics of the nonequilibrium depletion of the electronic ground state population─often termed the ground state hole─with ultrafast XSS and OTAS, revealing a restoration of the ground state equilibrium in 2.3 ps. This combined experimental and theoretical study provides a critical test of various density functional approximations in the description of bridged d8-d8 metal complexes. The results show that density functional theory calculations can reproduce the primary experimental observations if dispersion interactions are added, and a hybrid functional, which includes exact exchange, is used.
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Affiliation(s)
- Natalia E Powers-Riggs
- PULSE Institute, SLAC Accelerator National Laboratory, Stanford University, Stanford, California 94025, United States
| | - Benedikt O Birgisson
- Science Institute and Faculty of Physical Sciences, VR-III, University of Iceland, 107 Reykjavík, Iceland
| | - Sumana L Raj
- PULSE Institute, SLAC Accelerator National Laboratory, Stanford University, Stanford, California 94025, United States
| | - Elisa Biasin
- PULSE Institute, SLAC Accelerator National Laboratory, Stanford University, Stanford, California 94025, United States
| | - Philipp Lenzen
- Department of Physics, Technical University of Denmark, 2800 Lyngby, Denmark
| | | | - Morten Haubro
- Department of Physics, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Dagrún K V Tveiten
- Science Institute and Faculty of Physical Sciences, VR-III, University of Iceland, 107 Reykjavík, Iceland
| | - Robert W Hartsock
- PULSE Institute, SLAC Accelerator National Laboratory, Stanford University, Stanford, California 94025, United States
| | - Tim B van Driel
- LCLS, SLAC National Laboratory, Menlo Park, California 94025, United States
| | - Kristjan Kunnus
- LCLS, SLAC National Laboratory, Menlo Park, California 94025, United States
| | - Matthieu Chollet
- LCLS, SLAC National Laboratory, Menlo Park, California 94025, United States
| | - Joseph S Robinson
- LCLS, SLAC National Laboratory, Menlo Park, California 94025, United States
| | - Silke Nelson
- LCLS, SLAC National Laboratory, Menlo Park, California 94025, United States
| | - Ruaridh Forbes
- LCLS, SLAC National Laboratory, Menlo Park, California 94025, United States
| | - Kristoffer Haldrup
- Department of Physics, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Kasper S Pedersen
- Department of Chemistry, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Gianluca Levi
- Science Institute and Faculty of Physical Sciences, VR-III, University of Iceland, 107 Reykjavík, Iceland
| | - Asmus Ougaard Dohn
- PULSE Institute, SLAC Accelerator National Laboratory, Stanford University, Stanford, California 94025, United States
- Department of Physics, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Hannes Jónsson
- Science Institute and Faculty of Physical Sciences, VR-III, University of Iceland, 107 Reykjavík, Iceland
| | | | - Adi Natan
- PULSE Institute, SLAC Accelerator National Laboratory, Stanford University, Stanford, California 94025, United States
| | | | - Kelly J Gaffney
- PULSE Institute, SLAC Accelerator National Laboratory, Stanford University, Stanford, California 94025, United States
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3
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Ketawala G, Reiter CM, Fromme P, Botha S. The Pixel Anomaly Detection Tool: a user-friendly GUI for classifying detector frames using machine-learning approaches. J Appl Crystallogr 2024; 57:529-538. [PMID: 38596720 PMCID: PMC11001403 DOI: 10.1107/s1600576724000116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/03/2024] [Indexed: 04/11/2024] Open
Abstract
Data collection at X-ray free electron lasers has particular experimental challenges, such as continuous sample delivery or the use of novel ultrafast high-dynamic-range gain-switching X-ray detectors. This can result in a multitude of data artefacts, which can be detrimental to accurately determining structure-factor amplitudes for serial crystallography or single-particle imaging experiments. Here, a new data-classification tool is reported that offers a variety of machine-learning algorithms to sort data trained either on manual data sorting by the user or by profile fitting the intensity distribution on the detector based on the experiment. This is integrated into an easy-to-use graphical user interface, specifically designed to support the detectors, file formats and software available at most X-ray free electron laser facilities. The highly modular design makes the tool easily expandable to comply with other X-ray sources and detectors, and the supervised learning approach enables even the novice user to sort data containing unwanted artefacts or perform routine data-analysis tasks such as hit finding during an experiment, without needing to write code.
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Affiliation(s)
- Gihan Ketawala
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Caitlin M. Reiter
- NSF BioXFEL Science and Technology Center Summer Internship Program, NY 14203, USA
| | - Petra Fromme
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Sabine Botha
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
- Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA
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4
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Reinhard M, Gallo A, Guo M, Garcia-Esparza AT, Biasin E, Qureshi M, Britz A, Ledbetter K, Kunnus K, Weninger C, van Driel T, Robinson J, Glownia JM, Gaffney KJ, Kroll T, Weng TC, Alonso-Mori R, Sokaras D. Ferricyanide photo-aquation pathway revealed by combined femtosecond Kβ main line and valence-to-core x-ray emission spectroscopy. Nat Commun 2023; 14:2443. [PMID: 37147295 PMCID: PMC10163258 DOI: 10.1038/s41467-023-37922-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 03/30/2023] [Indexed: 05/07/2023] Open
Abstract
Reliably identifying short-lived chemical reaction intermediates is crucial to elucidate reaction mechanisms but becomes particularly challenging when multiple transient species occur simultaneously. Here, we report a femtosecond x-ray emission spectroscopy and scattering study of the aqueous ferricyanide photochemistry, utilizing the combined Fe Kβ main and valence-to-core emission lines. Following UV-excitation, we observe a ligand-to-metal charge transfer excited state that decays within 0.5 ps. On this timescale, we also detect a hitherto unobserved short-lived species that we assign to a ferric penta-coordinate intermediate of the photo-aquation reaction. We provide evidence that bond photolysis occurs from reactive metal-centered excited states that are populated through relaxation of the charge transfer excited state. Beyond illuminating the elusive ferricyanide photochemistry, these results show how current limitations of Kβ main line analysis in assigning ultrafast reaction intermediates can be circumvented by simultaneously using the valence-to-core spectral range.
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Affiliation(s)
- Marco Reinhard
- SLAC National Accelerator Laboratory, Menlo Park, CA, USA.
| | | | - Meiyuan Guo
- SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | | | - Elisa Biasin
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | | | | | - Kathryn Ledbetter
- Department of Physics, Stanford University, Stanford, CA, USA
- Department of Physics, Harvard University, Cambridge, MA, USA
| | | | - Clemens Weninger
- SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- MAX IV Laboratory, Lund University, Lund, Sweden
| | - Tim van Driel
- SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | | | | | | | - Thomas Kroll
- SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Tsu-Chien Weng
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
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5
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Peck A, Chang HY, Dujardin A, Ramalingam D, Uervirojnangkoorn M, Wang Z, Mancuso A, Poitevin F, Yoon CH. Skopi: a simulation package for diffractive imaging of noncrystalline biomolecules. J Appl Crystallogr 2022; 55:1002-1010. [PMID: 35974743 PMCID: PMC9348890 DOI: 10.1107/s1600576722005994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 06/03/2022] [Indexed: 11/10/2022] Open
Abstract
X-ray free-electron lasers (XFELs) have the ability to produce ultra-bright femtosecond X-ray pulses for coherent diffraction imaging of biomolecules. While the development of methods and algorithms for macromolecular crystallography is now mature, XFEL experiments involving aerosolized or solvated biomolecular samples offer new challenges in terms of both experimental design and data processing. Skopi is a simulation package that can generate single-hit diffraction images for reconstruction algorithms, multi-hit diffraction images of aggregated particles for training machine learning classifiers using labeled data, diffraction images of randomly distributed particles for fluctuation X-ray scattering algorithms, and diffraction images of reference and target particles for holographic reconstruction algorithms. Skopi is a resource to aid feasibility studies and advance the development of algorithms for noncrystalline experiments at XFEL facilities.
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Affiliation(s)
- Ariana Peck
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Hsing-Yin Chang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Antoine Dujardin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Deeban Ramalingam
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Monarin Uervirojnangkoorn
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Zhaoyou Wang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Adrian Mancuso
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Frédéric Poitevin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
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6
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Lee MC, Sirica N, Teitelbaum SW, Maznev A, Pezeril T, Tutchton R, Krapivin V, de la Pena GA, Huang Y, Zhao LX, Chen GF, Xu B, Yang R, Shi J, Zhu JX, Yarotski DA, Qiu XG, Nelson KA, Trigo M, Reis DA, Prasankumar RP. Direct Observation of Coherent Longitudinal and Shear Acoustic Phonons in TaAs Using Ultrafast X-Ray Diffraction. PHYSICAL REVIEW LETTERS 2022; 128:155301. [PMID: 35499894 DOI: 10.1103/physrevlett.128.155301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/19/2022] [Accepted: 02/25/2022] [Indexed: 06/14/2023]
Abstract
Using femtosecond time-resolved x-ray diffraction, we investigated optically excited coherent acoustic phonons in the Weyl semimetal TaAs. The low symmetry of the (112) surface probed in our experiment enables the simultaneous excitation of longitudinal and shear acoustic modes, whose dispersion closely matches our simulations. We observed an asymmetry in the spectral line shape of the longitudinal mode that is notably absent from the shear mode, suggesting a time-dependent frequency chirp that is likely driven by photoinduced carrier diffusion. We argue on the basis of symmetry that these acoustic deformations can transiently alter the electronic structure near the Weyl points and support this with model calculations. Our study underscores the benefit of using off-axis crystal orientations when optically exciting acoustic deformations in topological semimetals, allowing one to transiently change their crystal and electronic structures.
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Affiliation(s)
- Min-Cheol Lee
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - N Sirica
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - S W Teitelbaum
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
- Stanford Institute for Materials and Energy Sciences, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - A Maznev
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
- Institute for Soldier Nanotechnology, Massachusetts Institute of Technology, 500 Technology Square, NE47-598, Cambridge, Massachusetts, 02139, USA
| | - T Pezeril
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
- Institut de Physique de Rennes, Université de Rennes 1, UMR CNRS 6251, 35000 Rennes, France
| | - R Tutchton
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - V Krapivin
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
- Stanford Institute for Materials and Energy Sciences, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
- Department of Applied Physics, Stanford University, Stanford, California 94305, USA
| | - G A de la Pena
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
- Stanford Institute for Materials and Energy Sciences, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Y Huang
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
- Stanford Institute for Materials and Energy Sciences, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
- Department of Applied Physics, Stanford University, Stanford, California 94305, USA
| | - L X Zhao
- Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - G F Chen
- Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - B Xu
- Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - R Yang
- Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - J Shi
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - J-X Zhu
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - D A Yarotski
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - X G Qiu
- Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - K A Nelson
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
- Institute for Soldier Nanotechnology, Massachusetts Institute of Technology, 500 Technology Square, NE47-598, Cambridge, Massachusetts, 02139, USA
| | - M Trigo
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
- Stanford Institute for Materials and Energy Sciences, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - D A Reis
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
- Stanford Institute for Materials and Energy Sciences, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
- Department of Applied Physics, Stanford University, Stanford, California 94305, USA
- Department of Photon Science, Stanford University, Stanford, California 94305, USA
| | - R P Prasankumar
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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7
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Fransson T, Alonso-Mori R, Chatterjee R, Cheah MH, Ibrahim M, Hussein R, Zhang M, Fuller F, Gul S, Kim IS, Simon PS, Bogacz I, Makita H, de Lichtenberg C, Song S, Batyuk A, Sokaras D, Massad R, Doyle M, Britz A, Weninger C, Zouni A, Messinger J, Yachandra VK, Yano J, Kern J, Bergmann U. Effects of x-ray free-electron laser pulse intensity on the Mn K β 1,3 x-ray emission spectrum in photosystem II-A case study for metalloprotein crystals and solutions. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2021; 8:064302. [PMID: 34849380 PMCID: PMC8610604 DOI: 10.1063/4.0000130] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/24/2021] [Indexed: 05/21/2023]
Abstract
In the last ten years, x-ray free-electron lasers (XFELs) have been successfully employed to characterize metalloproteins at room temperature using various techniques including x-ray diffraction, scattering, and spectroscopy. The approach has been to outrun the radiation damage by using femtosecond (fs) x-ray pulses. An example of an important and damage sensitive active metal center is the Mn4CaO5 cluster in photosystem II (PS II), the catalytic site of photosynthetic water oxidation. The combination of serial femtosecond x-ray crystallography and Kβ x-ray emission spectroscopy (XES) has proven to be a powerful multimodal approach for simultaneously probing the overall protein structure and the electronic state of the Mn4CaO5 cluster throughout the catalytic (Kok) cycle. As the observed spectral changes in the Mn4CaO5 cluster are very subtle, it is critical to consider the potential effects of the intense XFEL pulses on the Kβ XES signal. We report here a systematic study of the effects of XFEL peak power, beam focus, and dose on the Mn Kβ1,3 XES spectra in PS II over a wide range of pulse parameters collected over seven different experimental runs using both microcrystal and solution PS II samples. Our findings show that for beam intensities ranging from ∼5 × 1015 to 5 × 1017 W/cm2 at a pulse length of ∼35 fs, the spectral effects are small compared to those observed between S-states in the Kok cycle. Our results provide a benchmark for other XFEL-based XES studies on metalloproteins, confirming the viability of this approach.
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Affiliation(s)
- Thomas Fransson
- Department of Theoretical Chemistry and Biology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Mun Hon Cheah
- Department of Chemistry – Ångström Laboratory, Molecular Biomimetics, Uppsala University, SE 75120 Uppsala, Sweden
| | - Mohamed Ibrahim
- Humboldt-Universität zu Berlin, Department of Biology, 10099 Berlin, Germany
| | - Rana Hussein
- Humboldt-Universität zu Berlin, Department of Biology, 10099 Berlin, Germany
| | - Miao Zhang
- Humboldt-Universität zu Berlin, Department of Biology, 10099 Berlin, Germany
| | - Franklin Fuller
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - In-Sik Kim
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Philipp S. Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Isabel Bogacz
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Hiroki Makita
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | | | - Sanghoon Song
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Dimosthenis Sokaras
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Ramzi Massad
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Margaret Doyle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | | | | | - Athina Zouni
- Humboldt-Universität zu Berlin, Department of Biology, 10099 Berlin, Germany
| | | | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Uwe Bergmann
- Department of Physics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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8
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Gorel A, Schlichting I, Barends TRM. Discerning best practices in XFEL-based biological crystallography - standards for nonstandard experiments. IUCRJ 2021; 8:532-543. [PMID: 34258002 PMCID: PMC8256713 DOI: 10.1107/s205225252100467x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/03/2021] [Indexed: 06/13/2023]
Abstract
Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) is a novel tool in structural biology. In contrast to conventional crystallography, SFX relies on merging partial intensities acquired with X-ray beams of often randomly fluctuating properties from a very large number of still diffraction images of generally randomly oriented microcrystals. For this reason, and possibly due to limitations of the still evolving data-analysis programs, XFEL-derived SFX data are typically of a lower quality than 'standard' crystallographic data. In contrast with this, the studies performed at XFELs often aim to investigate issues that require precise high-resolution data, for example to determine structures of intermediates at low occupancy, which often display very small conformational changes. This is a potentially dangerous combination and underscores the need for a critical evaluation of procedures including data-quality standards in XFEL-based structural biology. Here, such concerns are addressed.
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Affiliation(s)
- Alexander Gorel
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstr. 29, Heidelberg, 69120, Germany
| | - Ilme Schlichting
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstr. 29, Heidelberg, 69120, Germany
| | - Thomas R. M. Barends
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstr. 29, Heidelberg, 69120, Germany
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9
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Lahey-Rudolph JM, Schönherr R, Barthelmess M, Fischer P, Seuring C, Wagner A, Meents A, Redecke L. Fixed-target serial femtosecond crystallography using in cellulo grown microcrystals. IUCRJ 2021; 8:665-677. [PMID: 34258014 PMCID: PMC8256716 DOI: 10.1107/s2052252521005297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 05/18/2021] [Indexed: 05/05/2023]
Abstract
The crystallization of recombinant proteins in living cells is an exciting new approach in structural biology. Recent success has highlighted the need for fast and efficient diffraction data collection, optimally directly exposing intact crystal-containing cells to the X-ray beam, thus protecting the in cellulo crystals from environmental challenges. Serial femtosecond crystallography (SFX) at free-electron lasers (XFELs) allows the collection of detectable diffraction even from tiny protein crystals, but requires very fast sample exchange to utilize each XFEL pulse. Here, an efficient approach is presented for high-resolution structure elucidation using serial femtosecond in cellulo diffraction of micometre-sized crystals of the protein HEX-1 from the fungus Neurospora crassa on a fixed target. Employing the fast and highly accurate Roadrunner II translation-stage system allowed efficient raster scanning of the pores of micro-patterned, single-crystalline silicon chips loaded with living, crystal-containing insect cells. Compared with liquid-jet and LCP injection systems, the increased hit rates of up to 30% and reduced background scattering enabled elucidation of the HEX-1 structure. Using diffraction data from only a single chip collected within 12 min at the Linac Coherent Light Source, a 1.8 Å resolution structure was obtained with significantly reduced sample consumption compared with previous SFX experiments using liquid-jet injection. This HEX-1 structure is almost superimposable with that previously determined using synchrotron radiation from single HEX-1 crystals grown by sitting-drop vapour diffusion, validating the approach. This study demonstrates that fixed-target SFX using micro-patterned silicon chips is ideally suited for efficient in cellulo diffraction data collection using living, crystal-containing cells, and offers huge potential for the straightforward structure elucidation of proteins that form intracellular crystals at both XFELs and synchrotron sources.
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Affiliation(s)
- J. Mia Lahey-Rudolph
- Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Robert Schönherr
- Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
- Photon Science, Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Miriam Barthelmess
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Pontus Fischer
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Carolin Seuring
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, 22671 Hamburg, Germany
| | - Armin Wagner
- Diamond Light Source, Diamond House DH2-52, Chilton, Didcot OX11 0DE, United Kingdom
| | - Alke Meents
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
- Photon Science, Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Lars Redecke
- Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
- Photon Science, Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
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10
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Sorigué D, Hadjidemetriou K, Blangy S, Gotthard G, Bonvalet A, Coquelle N, Samire P, Aleksandrov A, Antonucci L, Benachir A, Boutet S, Byrdin M, Cammarata M, Carbajo S, Cuiné S, Doak RB, Foucar L, Gorel A, Grünbein M, Hartmann E, Hienerwadel R, Hilpert M, Kloos M, Lane TJ, Légeret B, Legrand P, Li-Beisson Y, Moulin SLY, Nurizzo D, Peltier G, Schirò G, Shoeman RL, Sliwa M, Solinas X, Zhuang B, Barends TRM, Colletier JP, Joffre M, Royant A, Berthomieu C, Weik M, Domratcheva T, Brettel K, Vos MH, Schlichting I, Arnoux P, Müller P, Beisson F. Mechanism and dynamics of fatty acid photodecarboxylase. Science 2021; 372:372/6538/eabd5687. [PMID: 33833098 DOI: 10.1126/science.abd5687] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 02/17/2021] [Indexed: 12/21/2022]
Abstract
Fatty acid photodecarboxylase (FAP) is a photoenzyme with potential green chemistry applications. By combining static, time-resolved, and cryotrapping spectroscopy and crystallography as well as computation, we characterized Chlorella variabilis FAP reaction intermediates on time scales from subpicoseconds to milliseconds. High-resolution crystal structures from synchrotron and free electron laser x-ray sources highlighted an unusual bent shape of the oxidized flavin chromophore. We demonstrate that decarboxylation occurs directly upon reduction of the excited flavin by the fatty acid substrate. Along with flavin reoxidation by the alkyl radical intermediate, a major fraction of the cleaved carbon dioxide unexpectedly transformed in 100 nanoseconds, most likely into bicarbonate. This reaction is orders of magnitude faster than in solution. Two strictly conserved residues, R451 and C432, are essential for substrate stabilization and functional charge transfer.
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Affiliation(s)
- D Sorigué
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - K Hadjidemetriou
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, 38000 Grenoble, France
| | - S Blangy
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - G Gotthard
- European Synchrotron Radiation Facility, 38043 Grenoble, France
| | - A Bonvalet
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - N Coquelle
- Large-Scale Structures Group, Institut Laue Langevin, 38042 Grenoble Cedex 9, France
| | - P Samire
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France.,Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - A Aleksandrov
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - L Antonucci
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - A Benachir
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - S Boutet
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - M Byrdin
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, 38000 Grenoble, France
| | - M Cammarata
- Department of Physics, UMR UR1-CNRS 6251, University of Rennes 1, F-Rennes, France.
| | - S Carbajo
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - S Cuiné
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - R B Doak
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - L Foucar
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - A Gorel
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - M Grünbein
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - E Hartmann
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - R Hienerwadel
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - M Hilpert
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - M Kloos
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany.
| | - T J Lane
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - B Légeret
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - P Legrand
- Synchrotron SOLEIL. L'Orme des Merisiers Saint-Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - Y Li-Beisson
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - S L Y Moulin
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - D Nurizzo
- European Synchrotron Radiation Facility, 38043 Grenoble, France
| | - G Peltier
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - G Schirò
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, 38000 Grenoble, France
| | - R L Shoeman
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - M Sliwa
- Univ. Lille, CNRS, UMR 8516, LASIRE, LAboratoire de Spectroscopie pour les Interactions, la Réactivité et l'Environnement, 59000 Lille, France
| | - X Solinas
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - B Zhuang
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France.,Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - T R M Barends
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - J-P Colletier
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, 38000 Grenoble, France
| | - M Joffre
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - A Royant
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, 38000 Grenoble, France.,European Synchrotron Radiation Facility, 38043 Grenoble, France
| | - C Berthomieu
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France.
| | - M Weik
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, 38000 Grenoble, France.
| | - T Domratcheva
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany. .,Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - K Brettel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - M H Vos
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France.
| | - I Schlichting
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany.
| | - P Arnoux
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France.
| | - P Müller
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - F Beisson
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France.
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11
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Short-lived metal-centered excited state initiates iron-methionine photodissociation in ferrous cytochrome c. Nat Commun 2021; 12:1086. [PMID: 33597529 PMCID: PMC7889893 DOI: 10.1038/s41467-021-21423-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 01/22/2021] [Indexed: 12/14/2022] Open
Abstract
The dynamics of photodissociation and recombination in heme proteins represent an archetypical photochemical reaction widely used to understand the interplay between chemical dynamics and reaction environment. We report a study of the photodissociation mechanism for the Fe(II)-S bond between the heme iron and methionine sulfur of ferrous cytochrome c. This bond dissociation is an essential step in the conversion of cytochrome c from an electron transfer protein to a peroxidase enzyme. We use ultrafast X-ray solution scattering to follow the dynamics of Fe(II)-S bond dissociation and 1s3p (Kβ) X-ray emission spectroscopy to follow the dynamics of the iron charge and spin multiplicity during bond dissociation. From these measurements, we conclude that the formation of a triplet metal-centered excited state with anti-bonding Fe(II)-S interactions triggers the bond dissociation and precedes the formation of the metastable Fe high-spin quintet state.
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12
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Wollenweber L, Preston TR, Descamps A, Cerantola V, Comley A, Eggert JH, Fletcher LB, Geloni G, Gericke DO, Glenzer SH, Göde S, Hastings J, Humphries OS, Jenei A, Karnbach O, Konopkova Z, Loetzsch R, Marx-Glowna B, McBride EE, McGonegle D, Monaco G, Ofori-Okai BK, Palmer CAJ, Plückthun C, Redmer R, Strohm C, Thorpe I, Tschentscher T, Uschmann I, Wark JS, White TG, Appel K, Gregori G, Zastrau U. High-resolution inelastic x-ray scattering at the high energy density scientific instrument at the European X-Ray Free-Electron Laser. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2021; 92:013101. [PMID: 33514249 DOI: 10.1063/5.0022886] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 12/12/2020] [Indexed: 06/12/2023]
Abstract
We introduce a setup to measure high-resolution inelastic x-ray scattering at the High Energy Density scientific instrument at the European X-Ray Free-Electron Laser (XFEL). The setup uses the Si (533) reflection in a channel-cut monochromator and three spherical diced analyzer crystals in near-backscattering geometry to reach a high spectral resolution. An energy resolution of 44 meV is demonstrated for the experimental setup, close to the theoretically achievable minimum resolution. The analyzer crystals and detector are mounted on a curved-rail system, allowing quick and reliable changes in scattering angle without breaking vacuum. The entire setup is designed for operation at 10 Hz, the same repetition rate as the high-power lasers available at the instrument and the fundamental repetition rate of the European XFEL. Among other measurements, it is envisioned that this setup will allow studies of the dynamics of highly transient laser generated states of matter.
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Affiliation(s)
- L Wollenweber
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - T R Preston
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - A Descamps
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - V Cerantola
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - A Comley
- Atomic Weapons Establishment, Aldermaston, Reading, Berkshire RG7 4PR, United Kingdom
| | - J H Eggert
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, USA
| | - L B Fletcher
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - G Geloni
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - D O Gericke
- Centre for Fusion, Space & Astrophysics, Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - S H Glenzer
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - S Göde
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - J Hastings
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - O S Humphries
- Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
| | - A Jenei
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, USA
| | - O Karnbach
- Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
| | - Z Konopkova
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - R Loetzsch
- Institut für Optik und Quantenelektronik, Friedrich-Schiller-Universität Jena, Max-Wien-Platz 1, 07743 Jena, Germany
| | - B Marx-Glowna
- Institut für Optik und Quantenelektronik, Friedrich-Schiller-Universität Jena, Max-Wien-Platz 1, 07743 Jena, Germany
| | - E E McBride
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - D McGonegle
- Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
| | - G Monaco
- Dipartimento di Fisica, Universita di Trento, via Sommarive 14, Povo 38123, TN, Italy
| | - B K Ofori-Okai
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - C A J Palmer
- School of Mathematics and Physics, Queen's University Belfast, University Road, BT7 1NN Belfast, United Kingdom
| | - C Plückthun
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - R Redmer
- Universität Rostock, Institut für Physik, Albert-Einstein-Straße 23-24, 18051 Rostock, Germany
| | - C Strohm
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - I Thorpe
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | - I Uschmann
- Institut für Optik und Quantenelektronik, Friedrich-Schiller-Universität Jena, Max-Wien-Platz 1, 07743 Jena, Germany
| | - J S Wark
- Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
| | - T G White
- Physics Department, University of Nevada at Reno, Reno, Nevada 89506, USA
| | - K Appel
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - G Gregori
- Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
| | - U Zastrau
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
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13
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Lee MY, Geiger J, Ishchenko A, Han GW, Barty A, White TA, Gati C, Batyuk A, Hunter MS, Aquila A, Boutet S, Weierstall U, Cherezov V, Liu W. Harnessing the power of an X-ray laser for serial crystallography of membrane proteins crystallized in lipidic cubic phase. IUCRJ 2020; 7:976-984. [PMID: 33209312 PMCID: PMC7642783 DOI: 10.1107/s2052252520012701] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 09/17/2020] [Indexed: 05/31/2023]
Abstract
Serial femtosecond crystallography (SFX) with X-ray free-electron lasers (XFELs) has proven highly successful for structure determination of challenging membrane proteins crystallized in lipidic cubic phase; however, like most techniques, it has limitations. Here we attempt to address some of these limitations related to the use of a vacuum chamber and the need for attenuation of the XFEL beam, in order to further improve the efficiency of this method. Using an optimized SFX experimental setup in a helium atmosphere, the room-temperature structure of the adenosine A2A receptor (A2AAR) at 2.0 Å resolution is determined and compared with previous A2AAR structures determined in vacuum and/or at cryogenic temperatures. Specifically, the capability of utilizing high XFEL beam transmissions is demonstrated, in conjunction with a high dynamic range detector, to collect high-resolution SFX data while reducing crystalline material consumption and shortening the collection time required for a complete dataset. The experimental setup presented herein can be applied to future SFX applications for protein nanocrystal samples to aid in structure-based discovery efforts of therapeutic targets that are difficult to crystallize.
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Affiliation(s)
- Ming-Yue Lee
- Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University, Tempe, AZ 85287-1604, USA
| | - James Geiger
- Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Andrii Ishchenko
- Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, 1002 W. Childs Way, Los Angeles, CA 90089, USA
| | - Gye Won Han
- Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, 1002 W. Childs Way, Los Angeles, CA 90089, USA
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Thomas A White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Cornelius Gati
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Alexander Batyuk
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Mark S Hunter
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Andrew Aquila
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Sébastien Boutet
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Uwe Weierstall
- Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Vadim Cherezov
- Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, 1002 W. Childs Way, Los Angeles, CA 90089, USA
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Wei Liu
- Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University, Tempe, AZ 85287-1604, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
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14
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Shelby M, Gilbile D, Grant T, Bauer W, Segelke B, He W, Evans A, Crespo N, Fischer P, Pakendorf T, Hennicke V, Hunter M, Batyuk A, Barthelmess M, Meents A, Kuhl T, Frank M, Coleman M. Crystallization of ApoA1 and ApoE4 nanolipoprotein particles and initial XFEL-based structural studies. CRYSTALS 2020; 10. [PMID: 35686136 PMCID: PMC9175823 DOI: 10.3390/cryst10100886] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nanolipoprotein particles (NLPs), also called “nanodiscs”, are discoidal particles with a patch of lipid bilayer corralled by apolipoproteins. NLPs have long been of interest due to both their utility as membrane-model systems into which membrane proteins can be inserted and solubilized and their physiological role in lipid and cholesterol transport via HDL and LDL maturation, which are important for human health. Serial femtosecond crystallography (SFX) at X-ray free electron lasers (XFELs) is a powerful approach for structural biology of membrane proteins, which are traditionally difficult to crystallize as large single crystals capable of producing high-quality diffraction suitable for structure determination. To facilitate understanding of the specific role of two apolipoprotein/lipid complexes, ApoA1 and ApoE4, in lipid binding and HDL/LDL particle maturation dynamics and develop new SFX methods involving NLP membrane protein encapsulation, we have prepared and crystallized homogeneous populations of ApoA1 and ApoE4 NLPs. Crystallization of empty NLPs yields semi-ordered objects that appear crystalline and give highly anisotropic and diffuse X-ray diffraction, similar in characteristics to fiber diffraction. Several unit cell parameters were approximately determined for both NLPs from these measurements. Thus, low-background, sample conservative methods of delivery are critical. Here we implemented a fixed target sample delivery scheme utilizing the Roadrunner fast-scanning system and ultra-thin polymer/graphene support films, providing a low-volume, low-background approach to membrane protein SFX. This study represents initial steps in obtaining structural information for ApoA1 and ApoE4 NLPs and developing this system as a supporting scaffold for future structural studies of membrane proteins crystalized in a native lipid environment.
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Affiliation(s)
- M.L. Shelby
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - D. Gilbile
- Department of Chemical Engineering, University of California at Davis, Davis, CA, USA
| | - T.D. Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, NY, USA
- Hauptman-Woodward Medical Research Institute, Buffalo, NY, USA
| | - W.J. Bauer
- Hauptman-Woodward Medical Research Institute, Buffalo, NY, USA
| | - B. Segelke
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - W. He
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - A.C. Evans
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Department of Chemical Engineering, University of California at Davis, Davis, CA, USA
| | - N. Crespo
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, NY, USA
- Hauptman-Woodward Medical Research Institute, Buffalo, NY, USA
| | - P. Fischer
- Center for Free-Electron Laser Science, Hamburg, Germany
| | - T. Pakendorf
- Center for Free-Electron Laser Science, Hamburg, Germany
| | - V. Hennicke
- Center for Free-Electron Laser Science, Hamburg, Germany
| | - M.S. Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - A. Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - M. Barthelmess
- Center for Free-Electron Laser Science, Hamburg, Germany
| | - A. Meents
- Center for Free-Electron Laser Science, Hamburg, Germany
| | - T.L. Kuhl
- Department of Chemical Engineering, University of California at Davis, Davis, CA, USA
| | - M. Frank
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Department of Chemical Engineering, University of California at Davis, Davis, CA, USA
- Correspondence: ; Tel: +1-925-423-7687 or ; Tel: 1-925-423-5068
| | - M.A. Coleman
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Department of Chemical Engineering, University of California at Davis, Davis, CA, USA
- Correspondence: ; Tel: +1-925-423-7687 or ; Tel: 1-925-423-5068
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15
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Pump-Probe Time-Resolved Serial Femtosecond Crystallography at X-Ray Free Electron Lasers. CRYSTALS 2020. [DOI: 10.3390/cryst10070628] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
With time-resolved crystallography (TRX), it is possible to follow the reaction dynamics in biological macromolecules by investigating the structure of transient states along the reaction coordinate. X-ray free electron lasers (XFELs) have enabled TRX experiments on previously uncharted femtosecond timescales. Here, we review the recent developments, opportunities, and challenges of pump-probe TRX at XFELs.
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16
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Frydrych S, Vorberger J, Hartley NJ, Schuster AK, Ramakrishna K, Saunders AM, van Driel T, Falcone RW, Fletcher LB, Galtier E, Gamboa EJ, Glenzer SH, Granados E, MacDonald MJ, MacKinnon AJ, McBride EE, Nam I, Neumayer P, Pak A, Voigt K, Roth M, Sun P, Gericke DO, Döppner T, Kraus D. Demonstration of X-ray Thomson scattering as diagnostics for miscibility in warm dense matter. Nat Commun 2020; 11:2620. [PMID: 32457297 PMCID: PMC7251136 DOI: 10.1038/s41467-020-16426-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 04/29/2020] [Indexed: 11/12/2022] Open
Abstract
The gas and ice giants in our solar system can be seen as a natural laboratory for the physics of highly compressed matter at temperatures up to thousands of kelvins. In turn, our understanding of their structure and evolution depends critically on our ability to model such matter. One key aspect is the miscibility of the elements in their interiors. Here, we demonstrate the feasibility of X-ray Thomson scattering to quantify the degree of species separation in a 1:1 carbon-hydrogen mixture at a pressure of ~150 GPa and a temperature of ~5000 K. Our measurements provide absolute values of the structure factor that encodes the microscopic arrangement of the particles. From these data, we find a lower limit of [Formula: see text]% of the carbon atoms forming isolated carbon clusters. In principle, this procedure can be employed for investigating the miscibility behaviour of any binary mixture at the high-pressure environment of planetary interiors, in particular, for non-crystalline samples where it is difficult to obtain conclusive results from X-ray diffraction. Moreover, this method will enable unprecedented measurements of mixing/demixing kinetics in dense plasma environments, e.g., induced by chemistry or hydrodynamic instabilities.
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Affiliation(s)
- S Frydrych
- Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
- Institut für Kernphysik, Technische Universität Darmstadt, Schlossgartenstraße 9, Darmstadt, 64289, Germany
| | - J Vorberger
- Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, Dresden, 01328, Germany
| | - N J Hartley
- Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, Dresden, 01328, Germany
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - A K Schuster
- Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, Dresden, 01328, Germany
- Institute of Solid State and Materials Physics, Technische Universität Dresden, Dresden, 01069, Germany
| | - K Ramakrishna
- Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, Dresden, 01328, Germany
- Institute of Solid State and Materials Physics, Technische Universität Dresden, Dresden, 01069, Germany
| | - A M Saunders
- Department of Physics, University of California, Berkeley, CA, 94720, USA
| | - T van Driel
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - R W Falcone
- Department of Physics, University of California, Berkeley, CA, 94720, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - L B Fletcher
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - E Galtier
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - E J Gamboa
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - S H Glenzer
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - E Granados
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - M J MacDonald
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
- University of Michigan, Ann Arbor, MI, 48109, USA
| | - A J MacKinnon
- Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - E E McBride
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
- European XFEL GmbH, Holzkoppel 4, Schenefeld, 22869, Germany
| | - I Nam
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - P Neumayer
- GSI Helmholtzzentrum für Schwerionenforschung, Planckstraße 1, Darmstadt, 64291, Germany
| | - A Pak
- Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - K Voigt
- Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, Dresden, 01328, Germany
- Institute of Solid State and Materials Physics, Technische Universität Dresden, Dresden, 01069, Germany
| | - M Roth
- Institut für Kernphysik, Technische Universität Darmstadt, Schlossgartenstraße 9, Darmstadt, 64289, Germany
| | - P Sun
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - D O Gericke
- Centre for Fusion, Space and Astrophysics, Department of Physics, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - T Döppner
- Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - D Kraus
- Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, Dresden, 01328, Germany.
- Institute of Solid State and Materials Physics, Technische Universität Dresden, Dresden, 01069, Germany.
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17
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Ma L, Yong H, Geiser JD, Moreno Carrascosa A, Goff N, Weber PM. Ultrafast x-ray and electron scattering of free molecules: A comparative evaluation. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2020; 7:034102. [PMID: 32637459 PMCID: PMC7316516 DOI: 10.1063/4.0000010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 06/08/2020] [Indexed: 05/09/2023]
Abstract
Resolving gas phase molecular motions with simultaneous spatial and temporal resolution is rapidly coming within the reach of x-ray Free Electron Lasers (XFELs) and Mega-electron-Volt (MeV) electron beams. These two methods enable scattering experiments that have yielded fascinating new results, and while both are important methods for determining transient molecular structures in photochemical reactions, it is important to understand their relative merits. In the present study, we evaluate the respective scattering cross sections of the two methods and simulate their ability to determine excited state molecular structures in light of currently existing XFEL and MeV source parameters. Using the example of optically excited N-methyl morpholine and simulating the scattering patterns with shot noise, we find that the currently achievable signals are superior with x-ray scattering for equal samples and on a per-shot basis and that x-ray scattering requires fewer detected signal counts for an equal fidelity structure determination. Importantly, within the independent atom model, excellent structure determinations can be achieved for scattering vectors only to about 5 Å-1, leaving larger scattering vector ranges for investigating vibrational motions and wavepackets. Electron scattering has a comparatively higher sensitivity toward hydrogen atoms, which may point to applications where electron scattering is inherently the preferred choice, provided that excellent signals can be achieved at large scattering angles that are currently difficult to access.
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Affiliation(s)
- Lingyu Ma
- Brown University, Department of Chemistry, Providence, Rhode Island 02912, USA
| | - Haiwang Yong
- Brown University, Department of Chemistry, Providence, Rhode Island 02912, USA
| | - Joseph D. Geiser
- Brown University, Department of Chemistry, Providence, Rhode Island 02912, USA
| | | | - Nathan Goff
- Brown University, Department of Chemistry, Providence, Rhode Island 02912, USA
| | - Peter M. Weber
- Brown University, Department of Chemistry, Providence, Rhode Island 02912, USA
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18
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van Driel TB, Nelson S, Armenta R, Blaj G, Boo S, Boutet S, Doering D, Dragone A, Hart P, Haller G, Kenney C, Kwaitowski M, Manger L, McKelvey M, Nakahara K, Oriunno M, Sato T, Weaver M. The ePix10k 2-megapixel hard X-ray detector at LCLS. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:608-615. [PMID: 32381760 PMCID: PMC7206547 DOI: 10.1107/s1600577520004257] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 03/27/2020] [Indexed: 05/25/2023]
Abstract
The ePix10ka2M (ePix10k) is a new large area detector specifically developed for X-ray free-electron laser (XFEL) applications. The hybrid pixel detector was developed at SLAC to provide a hard X-ray area detector with a high dynamic range, running at the 120 Hz repetition rate of the Linac Coherent Light Source (LCLS). The ePix10k consists of 16 modules, each with 352 × 384 pixels of 100 µm × 100 µm distributed on four ASICs, resulting in a 2.16 megapixel detector, with a 16.5 cm × 16.5 cm active area and ∼80% coverage. The high dynamic range is achieved with three distinct gain settings (low, medium, high) as well as two auto-ranging modes (high-to-low and medium-to-low). Here the three fixed gain modes are evaluated. The resulting dynamic range (from single photon counting to 10000 photons pixel-1 pulse-1 at 8 keV) makes it suitable for a large number of different XFEL experiments. The ePix10k replaces the large CSPAD in operation since 2011. The dimensions of the two detectors are similar, making the upgrade from CSPAD to ePix10k straightforward for most setups, with the ePix10k improving on experimental performance. The SLAC-developed ePix cameras all utilize a similar platform, are tailored to target different experimental conditions and are designed to provide an upgrade path for future high-repetition-rate XFELs. Here the first measurements on this new ePix10k detector are presented and the performance under typical XFEL conditions evaluated during an LCLS X-ray diffuse scattering experiment measuring the 9.5 keV X-ray photons scattered from a thin liquid jet.
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Affiliation(s)
- Tim Brandt van Driel
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Silke Nelson
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Rebecca Armenta
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Gabriel Blaj
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Stephen Boo
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Sébastien Boutet
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Dionisio Doering
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Angelo Dragone
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Philip Hart
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Gunther Haller
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Christopher Kenney
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Maciej Kwaitowski
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Leo Manger
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Mark McKelvey
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Kaz Nakahara
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Marco Oriunno
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Takahiro Sato
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Matt Weaver
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
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19
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Nass K, Gorel A, Abdullah MM, V Martin A, Kloos M, Marinelli A, Aquila A, Barends TRM, Decker FJ, Bruce Doak R, Foucar L, Hartmann E, Hilpert M, Hunter MS, Jurek Z, Koglin JE, Kozlov A, Lutman AA, Kovacs GN, Roome CM, Shoeman RL, Santra R, Quiney HM, Ziaja B, Boutet S, Schlichting I. Structural dynamics in proteins induced by and probed with X-ray free-electron laser pulses. Nat Commun 2020; 11:1814. [PMID: 32286284 PMCID: PMC7156470 DOI: 10.1038/s41467-020-15610-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 03/20/2020] [Indexed: 11/10/2022] Open
Abstract
X-ray free-electron lasers (XFELs) enable crystallographic structure determination beyond the limitations imposed upon synchrotron measurements by radiation damage. The need for very short XFEL pulses is relieved through gating of Bragg diffraction by loss of crystalline order as damage progresses, but not if ionization events are spatially non-uniform due to underlying elemental distributions, as in biological samples. Indeed, correlated movements of iron and sulfur ions were observed in XFEL-irradiated ferredoxin microcrystals using unusually long pulses of 80 fs. Here, we report a femtosecond time-resolved X-ray pump/X-ray probe experiment on protein nanocrystals. We observe changes in the protein backbone and aromatic residues as well as disulfide bridges. Simulations show that the latter’s correlated structural dynamics are much slower than expected for the predicted high atomic charge states due to significant impact of ion caging and plasma electron screening. This indicates that dense-environment effects can strongly affect local radiation damage-induced structural dynamics. The local X-ray-induced dynamics that occur in protein crystals during serial femtosecond crystallography (SFX) measurements at XFELs are not well understood. Here the authors performed a time-resolved X-ray pump X-ray probe SFX experiment, and they observe distinct structural changes in the disulfide bridges and peptide backbone of proteins; complementing theoretical approaches allow them to further characterize the details of the X-ray induced ionization and local structural dynamics.
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Affiliation(s)
- Karol Nass
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Alexander Gorel
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Malik M Abdullah
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Andrew V Martin
- School of Science, RMIT University, 124 La Trobe Street, Melbourne, VIC, 3000, Australia
| | - Marco Kloos
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | | | - Andrew Aquila
- SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Thomas R M Barends
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | | | - R Bruce Doak
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Lutz Foucar
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Elisabeth Hartmann
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Mario Hilpert
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Mark S Hunter
- SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Zoltan Jurek
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Jason E Koglin
- SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Alexander Kozlov
- ARC Centre of Excellence for Advanced Molecular Imaging, School of Physics, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Alberto A Lutman
- SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Gabriela Nass Kovacs
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Christopher M Roome
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Robert L Shoeman
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Robin Santra
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany.,Department of Physics, Universität Hamburg, Jungiusstrasse 9, 20355, Hamburg, Germany
| | - Harry M Quiney
- ARC Centre of Excellence for Advanced Molecular Imaging, School of Physics, The University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Beata Ziaja
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany. .,The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany. .,Institute of Nuclear Physics, Polish Academy of Sciences, Radzikowskiego 152, 31-342, Kraków, Poland.
| | - Sébastien Boutet
- SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Ilme Schlichting
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany.
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20
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Ledbetter K, Reinhard ME, Kunnus K, Gallo A, Britz A, Biasin E, Glownia JM, Nelson S, Van Driel TB, Weninger C, Zederkof DB, Haldrup K, Cordones AA, Gaffney KJ, Sokaras D, Alonso-Mori R. Excited state charge distribution and bond expansion of ferrous complexes observed with femtosecond valence-to-core x-ray emission spectroscopy. J Chem Phys 2020; 152:074203. [PMID: 32087640 DOI: 10.1063/1.5139441] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Valence-to-core x-ray emission spectroscopy (VtC XES) combines the sample flexibility and element specificity of hard x-rays with the chemical environment sensitivity of valence spectroscopy. We extend this technique to study geometric and electronic structural changes induced by photoexcitation in the femtosecond time domain via laser-pump, x-ray probe experiments using an x-ray free electron laser. The results of time-resolved VtC XES on a series of ferrous complexes [Fe(CN)2n(2, 2'-bipyridine)3-n]-2n+2, n = 1, 2, 3, are presented. Comparisons of spectra obtained from ground state density functional theory calculations reveal signatures of excited state bond length and oxidation state changes. An oxidation state change associated with a metal-to-ligand charge transfer state with a lifetime of less than 100 fs is observed, as well as bond length changes associated with metal-centered excited states with lifetimes of 13 ps and 250 ps.
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Affiliation(s)
- Kathryn Ledbetter
- Department of Physics, Stanford University, Stanford, California 94305, USA
| | - Marco E Reinhard
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Kristjan Kunnus
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Alessandro Gallo
- SUNCAT Center for Interface Science and Catalysis, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Alexander Britz
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Elisa Biasin
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - James M Glownia
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Silke Nelson
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Tim B Van Driel
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Clemens Weninger
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Diana B Zederkof
- Department of Physics, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Kristoffer Haldrup
- Department of Physics, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Amy A Cordones
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Kelly J Gaffney
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Dimosthenis Sokaras
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Roberto Alonso-Mori
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
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21
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Leonarski F, Mozzanica A, Brückner M, Lopez-Cuenca C, Redford S, Sala L, Babic A, Billich H, Bunk O, Schmitt B, Wang M. JUNGFRAU detector for brighter x-ray sources: Solutions for IT and data science challenges in macromolecular crystallography. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2020; 7:014305. [PMID: 32128347 PMCID: PMC7044001 DOI: 10.1063/1.5143480] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 02/04/2020] [Indexed: 05/08/2023]
Abstract
In this paper, we present a data workflow developed to operate the adJUstiNg Gain detector FoR the Aramis User station (JUNGFRAU) adaptive gain charge integrating pixel-array detectors at macromolecular crystallography beamlines. We summarize current achievements for operating at 9 GB/s data-rate a JUNGFRAU with 4 Mpixel at 1.1 kHz frame-rate and preparations to operate at 46 GB/s data-rate a JUNGFRAU with 10 Mpixel at 2.2 kHz in the future. In this context, we highlight the challenges for computer architecture and how these challenges can be addressed with innovative hardware including IBM POWER9 servers and field-programmable gate arrays. We discuss also data science challenges, showing the effect of rounding and lossy compression schemes on the MX JUNGFRAU detector images.
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Affiliation(s)
- Filip Leonarski
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Aldo Mozzanica
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Martin Brückner
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Carlos Lopez-Cuenca
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Sophie Redford
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Leonardo Sala
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Andrej Babic
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | | | - Oliver Bunk
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Bernd Schmitt
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Meitian Wang
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
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22
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Shelby ML, Gilbile D, Grant TD, Seuring C, Segelke BW, He W, Evans AC, Pakendorf T, Fischer P, Hunter MS, Batyuk A, Barthelmess M, Meents A, Coleman MA, Kuhl TL, Frank M. A fixed-target platform for serial femtosecond crystallography in a hydrated environment. IUCRJ 2020; 7:30-41. [PMID: 31949902 PMCID: PMC6949605 DOI: 10.1107/s2052252519014003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 10/15/2019] [Indexed: 05/19/2023]
Abstract
For serial femtosecond crystallography at X-ray free-electron lasers, which entails collection of single-pulse diffraction patterns from a constantly refreshed supply of microcrystalline sample, delivery of the sample into the X-ray beam path while maintaining low background remains a technical challenge for some experiments, especially where this methodology is applied to relatively low-ordered samples or those difficult to purify and crystallize in large quantities. This work demonstrates a scheme to encapsulate biological samples using polymer thin films and graphene to maintain sample hydration in vacuum conditions. The encapsulated sample is delivered into the X-ray beam on fixed targets for rapid scanning using the Roadrunner fixed-target system towards a long-term goal of low-background measurements on weakly diffracting samples. As a proof of principle, we used microcrystals of the 24 kDa rapid encystment protein (REP24) to provide a benchmark for polymer/graphene sandwich performance. The REP24 microcrystal unit cell obtained from our sandwiched in-vacuum sample was consistent with previously established unit-cell parameters and with those measured by us without encapsulation in humidified helium, indicating that the platform is robust against evaporative losses. While significant scattering from water was observed because of the sample-deposition method, the polymer/graphene sandwich itself was shown to contribute minimally to background scattering.
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Affiliation(s)
- M. L. Shelby
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - D. Gilbile
- University of California at Davis, California, USA
| | - T. D. Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, Hauptman-Woodward Institute, SUNY University at Buffalo, Buffalo, New York, USA
| | - C. Seuring
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - B. W. Segelke
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - W. He
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - A. C. Evans
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
- University of California at Davis, California, USA
| | - T. Pakendorf
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - P. Fischer
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - M. S. Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - A. Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - M. Barthelmess
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - A. Meents
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - M. A. Coleman
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
- University of California at Davis, California, USA
| | - T. L. Kuhl
- University of California at Davis, California, USA
| | - M. Frank
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
- University of California at Davis, California, USA
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23
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Core-level nonlinear spectroscopy triggered by stochastic X-ray pulses. Nat Commun 2019; 10:4761. [PMID: 31628306 PMCID: PMC6802401 DOI: 10.1038/s41467-019-12717-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 09/25/2019] [Indexed: 11/08/2022] Open
Abstract
Stochastic processes are highly relevant in research fields as different as neuroscience, economy, ecology, chemistry, and fundamental physics. However, due to their intrinsic unpredictability, stochastic mechanisms are very challenging for any kind of investigations and practical applications. Here we report the deliberate use of stochastic X-ray pulses in two-dimensional spectroscopy to the simultaneous mapping of unoccupied and occupied electronic states of atoms in a regime where the opacity and transparency properties of matter are subject to the incident intensity and photon energy. A readily transferable matrix formalism is presented to extract the electronic states from a dataset measured with the monitored input from a stochastic excitation source. The presented formalism enables investigations of the response of the electronic structure to irradiation with intense X-ray pulses while the time structure of the incident pulses is preserved.
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24
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Blaj G. Dead-time correction for spectroscopic photon-counting pixel detectors. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:1621-1630. [PMID: 31490152 DOI: 10.1107/s1600577519007409] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 05/21/2019] [Indexed: 06/10/2023]
Abstract
Modern photon-counting pixel detectors have enabled a revolution in applications at synchrotron light sources and beyond in the last decade. One of the limitations of the current detectors is their reduced counting linearity or even paralysis at high counting rates, due to dead-time which results in photon pile-up. Existing dead-time and pile-up models fail to reproduce the complexity of dead-time effects on photon-counting, resulting in empirical calibrations for particular detectors at best, imprecise linearization methods, or no linearization. This problem will increase in the future as many synchrotron light sources plan significant brilliance upgrades and free-electron lasers plan moving to a quasi-continuous operation mode. Presented here are the first models that use the actual behavior of the analog pre-amplifiers in spectroscopic photon-counting pixel detectors with constant current discharge (e.g. the Medipix and CPix families of detectors) to deduce more accurate analytical models and optimal linearization methods. In particular, for detectors with at least two counters per pixel, the need for calibration, or previous knowledge of the detector and beam parameters (dead-time, integration time, large sets of synchrotron filling patterns), is completely eliminated. This is summarized in several models of increasing complexity and accuracy. Finally, a general empirical approach is presented, applicable to any particular cases where the analytical approach is not sufficiently precise.
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Affiliation(s)
- Gabriel Blaj
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
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25
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Chatterjee R, Weninger C, Loukianov A, Gul S, Fuller FD, Cheah MH, Fransson T, Pham CC, Nelson S, Song S, Britz A, Messinger J, Bergmann U, Alonso-Mori R, Yachandra VK, Kern J, Yano J. XANES and EXAFS of dilute solutions of transition metals at XFELs. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:1716-1724. [PMID: 31490163 PMCID: PMC6730626 DOI: 10.1107/s1600577519007550] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 05/23/2019] [Indexed: 05/27/2023]
Abstract
This work has demonstrated that X-ray absorption spectroscopy (XAS), both Mn XANES and EXAFS, of solutions with millimolar concentrations of metal is possible using the femtosecond X-ray pulses from XFELs. Mn XAS data were collected using two different sample delivery methods, a Rayleigh jet and a drop-on-demand setup, with varying concentrations of Mn. Here, a new method for normalization of XAS spectra based on solvent scattering that is compatible with data collection from a highly variable pulsed source is described. The measured XANES and EXAFS spectra of such dilute solution samples are in good agreement with data collected at synchrotron sources using traditional scanning protocols. The procedures described here will enable XFEL-based XAS on dilute biological samples, especially metalloproteins, with low sample consumption. Details of the experimental setup and data analysis methods used in this XANES and EXAFS study are presented. This method will also benefit XAS performed at high-repetition-rate XFELs such as the European XFEL, LCLS-II and LCLS-II-HE.
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Affiliation(s)
- Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94704, USA
| | - Clemens Weninger
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Anton Loukianov
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94704, USA
| | - Franklin D. Fuller
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94704, USA
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Mun Hon Cheah
- Department of Chemistry – Ångström Laboratory, Molecular Biomimetics, Uppsala University, SE 75237 Uppsala, Sweden
| | - Thomas Fransson
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Cindy C. Pham
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94704, USA
| | - Silke Nelson
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Sanghoon Song
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Alexander Britz
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Johannes Messinger
- Department of Chemistry – Ångström Laboratory, Molecular Biomimetics, Uppsala University, SE 75237 Uppsala, Sweden
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden
| | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94704, USA
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94704, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94704, USA
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26
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Britz A, Abraham B, Biasin E, van Driel TB, Gallo A, Garcia-Esparza AT, Glownia J, Loukianov A, Nelson S, Reinhard M, Sokaras D, Alonso-Mori R. Resolving structures of transition metal complex reaction intermediates with femtosecond EXAFS. Phys Chem Chem Phys 2019; 22:2660-2666. [PMID: 31441480 DOI: 10.1039/c9cp03483h] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Femtosecond-resolved Extended X-ray Absorption Fine Structure (EXAFS) measurements of solvated transition metal complexes are successfully implemented at the X-ray Free Electron Laser LCLS. Benchmark experiments on [Fe(terpy)2]2+ in solution show a signal-to-noise ratio on the order of 500, comparable to typical 100 ps-resolution synchrotron measurements. In the few femtoseconds after photoexcitation, we observe the EXAFS fingerprints of a short-lived (∼100 fs) intermediate as well as those of a vibrationally hot long-lived (∼ns) excited state.
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Affiliation(s)
- Alexander Britz
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA. and Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
| | - Baxter Abraham
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA. and Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
| | - Elisa Biasin
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
| | - Tim Brandt van Driel
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
| | - Alessandro Gallo
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA and SUNCAT Center for Interface Science and Catalysis, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Angel T Garcia-Esparza
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
| | - James Glownia
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
| | - Anton Loukianov
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
| | - Silke Nelson
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
| | - Marco Reinhard
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
| | - Dimosthenis Sokaras
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
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27
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Nass Kovacs G, Colletier JP, Grünbein ML, Yang Y, Stensitzki T, Batyuk A, Carbajo S, Doak RB, Ehrenberg D, Foucar L, Gasper R, Gorel A, Hilpert M, Kloos M, Koglin JE, Reinstein J, Roome CM, Schlesinger R, Seaberg M, Shoeman RL, Stricker M, Boutet S, Haacke S, Heberle J, Heyne K, Domratcheva T, Barends TRM, Schlichting I. Three-dimensional view of ultrafast dynamics in photoexcited bacteriorhodopsin. Nat Commun 2019; 10:3177. [PMID: 31320619 PMCID: PMC6639342 DOI: 10.1038/s41467-019-10758-0] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 05/28/2019] [Indexed: 11/10/2022] Open
Abstract
Bacteriorhodopsin (bR) is a light-driven proton pump. The primary photochemical event upon light absorption is isomerization of the retinal chromophore. Here we used time-resolved crystallography at an X-ray free-electron laser to follow the structural changes in multiphoton-excited bR from 250 femtoseconds to 10 picoseconds. Quantum chemistry and ultrafast spectroscopy were used to identify a sequential two-photon absorption process, leading to excitation of a tryptophan residue flanking the retinal chromophore, as a first manifestation of multiphoton effects. We resolve distinct stages in the structural dynamics of the all-trans retinal in photoexcited bR to a highly twisted 13-cis conformation. Other active site sub-picosecond rearrangements include correlated vibrational motions of the electronically excited retinal chromophore, the surrounding amino acids and water molecules as well as their hydrogen bonding network. These results show that this extended photo-active network forms an electronically and vibrationally coupled system in bR, and most likely in all retinal proteins. Bacteriorhodopsin (bR) is a light-driven proton pump. Here the authors combine time-resolved crystallography at a free-electron laser, ultrafast spectroscopy and quantum chemistry to study the structural changes following multiphoton photoexcitation of bR and find that they occur within 300 fs not only in the light-absorbing chromophore but also in the surrounding protein.
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Affiliation(s)
- Gabriela Nass Kovacs
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Jacques-Philippe Colletier
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des Martyrs, 38000, Grenoble, France
| | - Marie Luise Grünbein
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Yang Yang
- Freie Universität Berlin, Department of Physics, Arnimallee 14, 14195, Berlin, Germany
| | - Till Stensitzki
- Freie Universität Berlin, Department of Physics, Arnimallee 14, 14195, Berlin, Germany
| | - Alexander Batyuk
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Sergio Carbajo
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - R Bruce Doak
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - David Ehrenberg
- Freie Universität Berlin, Department of Physics, Arnimallee 14, 14195, Berlin, Germany
| | - Lutz Foucar
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Raphael Gasper
- Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Str. 11, 44227, Dortmund, Germany
| | - Alexander Gorel
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Mario Hilpert
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Marco Kloos
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Jason E Koglin
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Jochen Reinstein
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Christopher M Roome
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Ramona Schlesinger
- Freie Universität Berlin, Department of Physics, Arnimallee 14, 14195, Berlin, Germany
| | - Matthew Seaberg
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Robert L Shoeman
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Miriam Stricker
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Sébastien Boutet
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Stefan Haacke
- Université de Strasbourg-CNRS, UMR 7504, IPCMS, 23 Rue du Loess, 67034, Strasbourg, France
| | - Joachim Heberle
- Freie Universität Berlin, Department of Physics, Arnimallee 14, 14195, Berlin, Germany
| | - Karsten Heyne
- Freie Universität Berlin, Department of Physics, Arnimallee 14, 14195, Berlin, Germany
| | - Tatiana Domratcheva
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany.
| | - Thomas R M Barends
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Ilme Schlichting
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany.
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28
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Casadei CM, Nass K, Barty A, Hunter MS, Padeste C, Tsai CJ, Boutet S, Messerschmidt M, Sala L, Williams GJ, Ozerov D, Coleman M, Li XD, Frank M, Pedrini B. Structure-factor amplitude reconstruction from serial femtosecond crystallography of two-dimensional membrane-protein crystals. IUCRJ 2019; 6:34-45. [PMID: 30713701 PMCID: PMC6327180 DOI: 10.1107/s2052252518014641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 10/16/2018] [Indexed: 06/09/2023]
Abstract
Serial femtosecond crystallography of two-dimensional membrane-protein crystals at X-ray free-electron lasers has the potential to address the dynamics of functionally relevant large-scale motions, which can be sterically hindered in three-dimensional crystals and suppressed in cryocooled samples. In previous work, diffraction data limited to a two-dimensional reciprocal-space slice were evaluated and it was demonstrated that the low intensity of the diffraction signal can be overcome by collecting highly redundant data, thus enhancing the achievable resolution. Here, the application of a newly developed method to analyze diffraction data covering three reciprocal-space dimensions, extracting the reciprocal-space map of the structure-factor amplitudes, is presented. Despite the low resolution and completeness of the data set, it is shown by molecular replacement that the reconstructed amplitudes carry meaningful structural information. Therefore, it appears that these intrinsic limitations in resolution and completeness from two-dimensional crystal diffraction may be overcome by collecting highly redundant data along the three reciprocal-space axes, thus allowing the measurement of large-scale dynamics in pump-probe experiments.
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Affiliation(s)
| | - Karol Nass
- Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Anton Barty
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Mark S. Hunter
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | | | - Ching-Ju Tsai
- Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Sébastien Boutet
- Linac Coherent Light Source, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Marc Messerschmidt
- Linac Coherent Light Source, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- National Science Foundation BioXFEL Science and Technology Center, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Leonardo Sala
- Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Garth J. Williams
- Linac Coherent Light Source, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- NSLS-II, Brookhaven National Laboratory, PO Box 5000, Upton, NY 11973, USA
| | - Dmitry Ozerov
- Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Matthew Coleman
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Xiao-Dan Li
- Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Matthias Frank
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Bill Pedrini
- Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
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29
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Yong H, Zotev N, Stankus B, Ruddock JM, Bellshaw D, Boutet S, Lane TJ, Liang M, Carbajo S, Robinson JS, Du W, Goff N, Chang Y, Koglin JE, Waters MDJ, Sølling TI, Minitti MP, Kirrander A, Weber PM. Determining Orientations of Optical Transition Dipole Moments Using Ultrafast X-ray Scattering. J Phys Chem Lett 2018; 9:6556-6562. [PMID: 30380873 DOI: 10.1021/acs.jpclett.8b02773] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Identification of the initially prepared, optically active state remains a challenging problem in many studies of ultrafast photoinduced processes. We show that the initially excited electronic state can be determined using the anisotropic component of ultrafast time-resolved X-ray scattering signals. The concept is demonstrated using the time-dependent X-ray scattering of N-methyl morpholine in the gas phase upon excitation by a 200 nm linearly polarized optical pulse. Analysis of the angular dependence of the scattering signal near time zero renders the orientation of the transition dipole moment in the molecular frame and identifies the initially excited state as the 3p z Rydberg state, thus bypassing the need for further experimental studies to determine the starting point of the photoinduced dynamics and clarifying inconsistent computational results.
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Affiliation(s)
- Haiwang Yong
- Department of Chemistry , Brown University , Providence , Rhode Island 02912 , United States
| | - Nikola Zotev
- School of Chemistry , University of Edinburgh , Edinburgh EH9 3FJ , United Kingdom
| | - Brian Stankus
- Department of Chemistry , Brown University , Providence , Rhode Island 02912 , United States
| | - Jennifer M Ruddock
- Department of Chemistry , Brown University , Providence , Rhode Island 02912 , United States
| | - Darren Bellshaw
- School of Chemistry , University of Edinburgh , Edinburgh EH9 3FJ , United Kingdom
| | - Sébastien Boutet
- SLAC National Accelerator Laboratory , Menlo Park , California 94025 , United States
| | - Thomas J Lane
- SLAC National Accelerator Laboratory , Menlo Park , California 94025 , United States
| | - Mengning Liang
- SLAC National Accelerator Laboratory , Menlo Park , California 94025 , United States
| | - Sergio Carbajo
- SLAC National Accelerator Laboratory , Menlo Park , California 94025 , United States
| | - Joseph S Robinson
- SLAC National Accelerator Laboratory , Menlo Park , California 94025 , United States
| | - Wenpeng Du
- Department of Chemistry , Brown University , Providence , Rhode Island 02912 , United States
| | - Nathan Goff
- Department of Chemistry , Brown University , Providence , Rhode Island 02912 , United States
| | - Yu Chang
- Department of Chemistry , Brown University , Providence , Rhode Island 02912 , United States
| | - Jason E Koglin
- SLAC National Accelerator Laboratory , Menlo Park , California 94025 , United States
| | - Max D J Waters
- Department of Chemistry , University of Copenhagen , Universitetsparken 5 , 2100 Copenhagen , Denmark
| | - Theis I Sølling
- Department of Chemistry , University of Copenhagen , Universitetsparken 5 , 2100 Copenhagen , Denmark
| | - Michael P Minitti
- SLAC National Accelerator Laboratory , Menlo Park , California 94025 , United States
| | - Adam Kirrander
- School of Chemistry , University of Edinburgh , Edinburgh EH9 3FJ , United Kingdom
| | - Peter M Weber
- Department of Chemistry , Brown University , Providence , Rhode Island 02912 , United States
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30
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McBride EE, White TG, Descamps A, Fletcher LB, Appel K, Condamine FP, Curry CB, Dallari F, Funk S, Galtier E, Gamboa EJ, Gauthier M, Goede S, Kim JB, Lee HJ, Ofori-Okai BK, Oliver M, Rigby A, Schoenwaelder C, Sun P, Tschentscher T, Witte BBL, Zastrau U, Gregori G, Nagler B, Hastings J, Glenzer SH, Monaco G. Setup for meV-resolution inelastic X-ray scattering measurements and X-ray diffraction at the Matter in Extreme Conditions endstation at the Linac Coherent Light Source. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2018; 89:10F104. [PMID: 30399942 DOI: 10.1063/1.5039329] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 06/20/2018] [Indexed: 06/08/2023]
Abstract
We describe a setup for performing inelastic X-ray scattering and X-ray diffraction measurements at the Matter in Extreme Conditions (MEC) endstation of the Linac Coherent Light Source. This technique is capable of performing high-, meV-resolution measurements of dynamic ion features in both crystalline and non-crystalline materials. A four-bounce silicon (533) monochromator was used in conjunction with three silicon (533) diced crystal analyzers to provide an energy resolution of ∼50 meV over a range of ∼500 meV in single shot measurements. In addition to the instrument resolution function, we demonstrate the measurement of longitudinal acoustic phonon modes in polycrystalline diamond. Furthermore, this setup may be combined with the high intensity laser drivers available at MEC to create warm dense matter and subsequently measure ion acoustic modes.
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Affiliation(s)
- E E McBride
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - T G White
- University of Nevada at Reno, Reno, Nevada 89506, USA
| | - A Descamps
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - L B Fletcher
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - K Appel
- European XFEL GmbH, Holzkoppel 4, D-22869 Schenefeld, Germany
| | - F P Condamine
- Sorbonne Universités, UPMC, LULI, UMR 7605, Case 128, 4 Place Jussieu, 75252 Paris Cedex 05, France
| | - C B Curry
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - F Dallari
- Dipartimento di Fisica, Università di Trento, via Sommarive 14, Povo 38123, TN, Italy
| | - S Funk
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen Centre for Astroparticle Physics, Erwin-Rommel-Str. 1, D-91058 Erlangen, Germany
| | - E Galtier
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | | | - M Gauthier
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - S Goede
- European XFEL GmbH, Holzkoppel 4, D-22869 Schenefeld, Germany
| | - J B Kim
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - H J Lee
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - B K Ofori-Okai
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - M Oliver
- Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
| | - A Rigby
- Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
| | - C Schoenwaelder
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - P Sun
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Th Tschentscher
- European XFEL GmbH, Holzkoppel 4, D-22869 Schenefeld, Germany
| | - B B L Witte
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - U Zastrau
- European XFEL GmbH, Holzkoppel 4, D-22869 Schenefeld, Germany
| | - G Gregori
- Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
| | - B Nagler
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - J Hastings
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - S H Glenzer
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - G Monaco
- Dipartimento di Fisica, Università di Trento, via Sommarive 14, Povo 38123, TN, Italy
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31
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Opara NL, Mohacsi I, Makita M, Castano-Diez D, Diaz A, Juranić P, Marsh M, Meents A, Milne CJ, Mozzanica A, Padeste C, Panneels V, Sikorski M, Song S, Stahlberg H, Vartiainen I, Vera L, Wang M, Willmott PR, David C. Demonstration of femtosecond X-ray pump X-ray probe diffraction on protein crystals. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2018; 5:054303. [PMID: 30364211 PMCID: PMC6192410 DOI: 10.1063/1.5050618] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 09/12/2018] [Indexed: 05/24/2023]
Abstract
The development of X-ray free-electron lasers (XFELs) has opened the possibility to investigate the ultrafast dynamics of biomacromolecules using X-ray diffraction. Whereas an increasing number of structures solved by means of serial femtosecond crystallography at XFELs is available, the effect of radiation damage on protein crystals during ultrafast exposures has remained an open question. We used a split-and-delay line based on diffractive X-ray optics at the Linac Coherent Light Source XFEL to investigate the time dependence of X-ray radiation damage to lysozyme crystals. For these tests, crystals were delivered to the X-ray beam using a fixed-target approach. The presented experiments provide probe signals at eight different delay times between 19 and 213 femtoseconds after a single pump event, thereby covering the time-scales relevant for femtosecond serial crystallography. Even though significant impact on the crystals was observed at long time scales after exposure with a single X-ray pulse, the collected diffraction data did not show significant signal reduction that could be assigned to beam damage on the crystals in the sampled time window and resolution range. This observation is in agreement with estimations of the applied radiation dose, which in our experiment was clearly below the values expected to cause damage on the femtosecond time scale. The experiments presented here demonstrate the feasibility of time-resolved pump-multiprobe X-ray diffraction experiments on protein crystals.
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Affiliation(s)
| | | | | | | | - Ana Diaz
- Paul Scherrer Institut, CH-5232 Villigen-PSI, Switzerland
| | - Pavle Juranić
- Paul Scherrer Institut, CH-5232 Villigen-PSI, Switzerland
| | - May Marsh
- Paul Scherrer Institut, CH-5232 Villigen-PSI, Switzerland
| | - Alke Meents
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, D-22607 Hamburg, Germany
| | | | - Aldo Mozzanica
- Paul Scherrer Institut, CH-5232 Villigen-PSI, Switzerland
| | | | | | - Marcin Sikorski
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Sanghoon Song
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | | | | | - Laura Vera
- Paul Scherrer Institut, CH-5232 Villigen-PSI, Switzerland
| | - Meitian Wang
- Paul Scherrer Institut, CH-5232 Villigen-PSI, Switzerland
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32
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Fransson T, Chatterjee R, Fuller FD, Gul S, Weninger C, Sokaras D, Kroll T, Alonso-Mori R, Bergmann U, Kern J, Yachandra VK, Yano J. X-ray Emission Spectroscopy as an in Situ Diagnostic Tool for X-ray Crystallography of Metalloproteins Using an X-ray Free-Electron Laser. Biochemistry 2018; 57:4629-4637. [PMID: 29906115 DOI: 10.1021/acs.biochem.8b00325] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Serial femtosecond crystallography (SFX) using the ultrashort X-ray pulses from a X-ray free-electron laser (XFEL) provides a new way of collecting structural data at room temperature that allows for following the reaction in real time after initiation. XFEL experiments are conducted in a shot-by-shot mode as the sample is destroyed and replenished after each X-ray pulse, and therefore, monitoring and controlling the data quality by using in situ diagnostic tools is critical. To study metalloenzymes, we developed the use of simultaneous collection of X-ray diffraction of crystals along with X-ray emission spectroscopy (XES) data that is used as a diagnostic tool for crystallography, by monitoring the chemical state of the metal catalytic center. We have optimized data analysis methods and sample delivery techniques for fast and active feedback to ensure the quality of each batch of samples and the turnover of the catalytic reaction caused by reaction triggering methods. Here, we describe this active in situ feedback system using Photosystem II as an example that catalyzes the oxidation of H2O to O2 at the Mn4CaO5 active site. We used the first moments of the Mn Kβ1,3 emission spectra, which are sensitive to the oxidation state of Mn, as the primary diagnostics. This approach is applicable to different metalloproteins to determine the integrity of samples and follow changes in the chemical states of the reaction that can be initiated by light or activated by substrates and offers a metric for determining the diffraction images that are used for the final data sets.
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Affiliation(s)
- Thomas Fransson
- Stanford PULSE Institute, SLAC National Accelerator Laboratory , Menlo Park , California United States
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California United States
| | - Franklin D Fuller
- LCLS, SLAC National Accelerator Laboratory , Menlo Park , California United States
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California United States
| | - Clemens Weninger
- LCLS, SLAC National Accelerator Laboratory , Menlo Park , California United States
| | - Dimosthenis Sokaras
- SSRL, SLAC National Accelerator Laboratory , Menlo Park , California United States
| | - Thomas Kroll
- SSRL, SLAC National Accelerator Laboratory , Menlo Park , California United States
| | - Roberto Alonso-Mori
- LCLS, SLAC National Accelerator Laboratory , Menlo Park , California United States
| | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory , Menlo Park , California United States
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California United States
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California United States
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California United States
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33
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Ke TW, Brewster AS, Yu SX, Ushizima D, Yang C, Sauter NK. A convolutional neural network-based screening tool for X-ray serial crystallography. JOURNAL OF SYNCHROTRON RADIATION 2018; 25:655-670. [PMID: 29714177 PMCID: PMC5929353 DOI: 10.1107/s1600577518004873] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 03/26/2018] [Indexed: 05/24/2023]
Abstract
A new tool is introduced for screening macromolecular X-ray crystallography diffraction images produced at an X-ray free-electron laser light source. Based on a data-driven deep learning approach, the proposed tool executes a convolutional neural network to detect Bragg spots. Automatic image processing algorithms described can enable the classification of large data sets, acquired under realistic conditions consisting of noisy data with experimental artifacts. Outcomes are compared for different data regimes, including samples from multiple instruments and differing amounts of training data for neural network optimization.
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Affiliation(s)
- Tsung-Wei Ke
- International Computer Science Institute, University of California Berkeley, Berkeley, CA 94704, USA
| | - Aaron S. Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Stella X. Yu
- International Computer Science Institute, University of California Berkeley, Berkeley, CA 94704, USA
| | - Daniela Ushizima
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Berkeley Institute for Data Science, University of California Berkeley, Berkeley, CA 94704, USA
| | - Chao Yang
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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34
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Current Status of Single Particle Imaging with X-ray Lasers. APPLIED SCIENCES-BASEL 2018. [DOI: 10.3390/app8010132] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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35
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Casadei CM, Tsai CJ, Barty A, Hunter MS, Zatsepin NA, Padeste C, Capitani G, Benner WH, Boutet S, Hau-Riege SP, Kupitz C, Messerschmidt M, Ogren JI, Pardini T, Rothschild KJ, Sala L, Segelke B, Williams GJ, Evans JE, Li XD, Coleman M, Pedrini B, Frank M. Resolution extension by image summing in serial femtosecond crystallography of two-dimensional membrane-protein crystals. IUCRJ 2018; 5:103-117. [PMID: 29354276 PMCID: PMC5755582 DOI: 10.1107/s2052252517017043] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 11/27/2017] [Indexed: 05/08/2023]
Abstract
Previous proof-of-concept measurements on single-layer two-dimensional membrane-protein crystals performed at X-ray free-electron lasers (FELs) have demonstrated that the collection of meaningful diffraction patterns, which is not possible at synchrotrons because of radiation-damage issues, is feasible. Here, the results obtained from the analysis of a thousand single-shot, room-temperature X-ray FEL diffraction images from two-dimensional crystals of a bacteriorhodopsin mutant are reported in detail. The high redundancy in the measurements boosts the intensity signal-to-noise ratio, so that the values of the diffracted intensities can be reliably determined down to the detector-edge resolution of 4 Å. The results show that two-dimensional serial crystallography at X-ray FELs is a suitable method to study membrane proteins to near-atomic length scales at ambient temperature. The method presented here can be extended to pump-probe studies of optically triggered structural changes on submillisecond timescales in two-dimensional crystals, which allow functionally relevant large-scale motions that may be quenched in three-dimensional crystals.
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Affiliation(s)
| | - Ching-Ju Tsai
- Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Anton Barty
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Mark S. Hunter
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Nadia A. Zatsepin
- Arizona State University, 300 East University Drive, Tempe, AZ 85287, USA
| | | | | | - W. Henry Benner
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Stefan P. Hau-Riege
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Christopher Kupitz
- Arizona State University, 300 East University Drive, Tempe, AZ 85287, USA
| | - Marc Messerschmidt
- Linac Coherent Light Source, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- National Science Foundation BioXFEL Science and Technology Center, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - John I. Ogren
- Physics Departement, Boston University, 590 Commonwealth Avenue, Boston, MA 02215, USA
| | - Tom Pardini
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Kenneth J. Rothschild
- Physics Departement, Boston University, 590 Commonwealth Avenue, Boston, MA 02215, USA
| | - Leonardo Sala
- Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Brent Segelke
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Garth J. Williams
- Linac Coherent Light Source, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - James E. Evans
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Boulevard, Richland, WA 99354, USA
| | - Xiao-Dan Li
- Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Matthew Coleman
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Bill Pedrini
- Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Matthias Frank
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
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36
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Seddon EA, Clarke JA, Dunning DJ, Masciovecchio C, Milne CJ, Parmigiani F, Rugg D, Spence JCH, Thompson NR, Ueda K, Vinko SM, Wark JS, Wurth W. Short-wavelength free-electron laser sources and science: a review. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2017; 80:115901. [PMID: 29059048 DOI: 10.1088/1361-6633/aa7cca] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
This review is focused on free-electron lasers (FELs) in the hard to soft x-ray regime. The aim is to provide newcomers to the area with insights into: the basic physics of FELs, the qualities of the radiation they produce, the challenges of transmitting that radiation to end users and the diversity of current scientific applications. Initial consideration is given to FEL theory in order to provide the foundation for discussion of FEL output properties and the technical challenges of short-wavelength FELs. This is followed by an overview of existing x-ray FEL facilities, future facilities and FEL frontiers. To provide a context for information in the above sections, a detailed comparison of the photon pulse characteristics of FEL sources with those of other sources of high brightness x-rays is made. A brief summary of FEL beamline design and photon diagnostics then precedes an overview of FEL scientific applications. Recent highlights are covered in sections on structural biology, atomic and molecular physics, photochemistry, non-linear spectroscopy, shock physics, solid density plasmas. A short industrial perspective is also included to emphasise potential in this area.
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Affiliation(s)
- E A Seddon
- ASTeC, STFC Daresbury Laboratory, Sci-Tech Daresbury, Keckwick Lane, Daresbury, Cheshire, WA4 4AD, United Kingdom. The School of Physics and Astronomy and Photon Science Institute, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom. The Cockcroft Institute, Sci-Tech Daresbury, Keckwick Lane, Daresbury, Cheshire, WA4 4AD, United Kingdom
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37
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Pietrini A, Nettelblad C. Artifact reduction in the CSPAD detectors used for LCLS experiments. JOURNAL OF SYNCHROTRON RADIATION 2017; 24:1092-1097. [PMID: 28862634 DOI: 10.1107/s160057751701058x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/18/2017] [Indexed: 06/07/2023]
Abstract
The existence of noise and column-wise artifacts in the CSPAD-140K detector and in a module of the CSPAD-2.3M large camera, respectively, is reported for the L730 and L867 experiments performed at the CXI Instrument at the Linac Coherent Light Source (LCLS), in low-flux and low signal-to-noise ratio regime. Possible remedies are discussed and an additional step in the preprocessing of data is introduced, which consists of performing a median subtraction along the columns of the detector modules. Thus, we reduce the overall variation in the photon count distribution, lowering the mean false-positive photon detection rate by about 4% (from 5.57 × 10-5 to 5.32 × 10-5 photon counts pixel-1 frame-1 in L867, cxi86715) and 7% (from 1.70 × 10-3 to 1.58 × 10-3 photon counts pixel-1 frame-1 in L730, cxi73013), and the standard deviation in false-positive photon count per shot by 15% and 35%, while not making our average photon detection threshold more stringent. Such improvements in detector noise reduction and artifact removal constitute a step forward in the development of flash X-ray imaging techniques for high-resolution, low-signal and in serial nano-crystallography experiments at X-ray free-electron laser facilities.
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Affiliation(s)
- Alberto Pietrini
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala 751 24, Sweden
| | - Carl Nettelblad
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala 751 24, Sweden
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38
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Johansson LC, Stauch B, Ishchenko A, Cherezov V. A Bright Future for Serial Femtosecond Crystallography with XFELs. Trends Biochem Sci 2017; 42:749-762. [PMID: 28733116 DOI: 10.1016/j.tibs.2017.06.007] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 06/12/2017] [Accepted: 06/20/2017] [Indexed: 11/19/2022]
Abstract
X-ray free electron lasers (XFELs) have the potential to revolutionize macromolecular structural biology due to the unique combination of spatial coherence, extreme peak brilliance, and short duration of X-ray pulses. A recently emerged serial femtosecond (fs) crystallography (SFX) approach using XFEL radiation overcomes some of the biggest hurdles of traditional crystallography related to radiation damage through the diffraction-before-destruction principle. Intense fs XFEL pulses enable high-resolution room-temperature structure determination of difficult-to-crystallize biological macromolecules, while simultaneously opening a new era of time-resolved structural studies. Here, we review the latest developments in instrumentation, sample delivery, data analysis, crystallization methods, and applications of SFX to important biological questions, and conclude with brief insights into the bright future of structural biology using XFELs.
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Affiliation(s)
- Linda C Johansson
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089-3303, USA
| | - Benjamin Stauch
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089-3303, USA
| | - Andrii Ishchenko
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089-3303, USA
| | - Vadim Cherezov
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089-3303, USA.
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39
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Double-flow focused liquid injector for efficient serial femtosecond crystallography. Sci Rep 2017; 7:44628. [PMID: 28300169 PMCID: PMC5353652 DOI: 10.1038/srep44628] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 02/10/2017] [Indexed: 01/12/2023] Open
Abstract
Serial femtosecond crystallography requires reliable and efficient delivery of fresh crystals across the beam of an X-ray free-electron laser over the course of an experiment. We introduce a double-flow focusing nozzle to meet this challenge, with significantly reduced sample consumption, while improving jet stability over previous generations of nozzles. We demonstrate its use to determine the first room-temperature structure of RNA polymerase II at high resolution, revealing new structural details. Moreover, the double-flow focusing nozzles were successfully tested with three other protein samples and the first room temperature structure of an extradiol ring-cleaving dioxygenase was solved by utilizing the improved operation and characteristics of these devices [corrected].
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40
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41
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Thayer J, Damiani D, Ford C, Dubrovin M, Gaponenko I, O’Grady CP, Kroeger W, Pines J, Lane TJ, Salnikov A, Schneider D, Tookey T, Weaver M, Yoon CH, Perazzo A. Data systems for the Linac coherent light source. ADVANCED STRUCTURAL AND CHEMICAL IMAGING 2017; 3:3. [PMID: 28261541 PMCID: PMC5313569 DOI: 10.1186/s40679-016-0037-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 12/28/2016] [Indexed: 11/10/2022]
Abstract
The data systems for X-ray free-electron laser (FEL) experiments at the Linac coherent light source (LCLS) are described. These systems are designed to acquire and to reliably transport shot-by-shot data at a peak throughput of 5 GB/s to the offline data storage where experimental data and the relevant metadata are archived and made available for user analysis. The analysis and monitoring implementation (AMI) and Photon Science ANAlysis (psana) software packages are described. Psana is open source and freely available.
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Affiliation(s)
- J. Thayer
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 USA
| | - D. Damiani
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 USA
| | - C. Ford
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 USA
| | - M. Dubrovin
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 USA
| | - I. Gaponenko
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 USA
| | - C. P. O’Grady
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 USA
| | - W. Kroeger
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 USA
| | - J. Pines
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 USA
| | - T. J. Lane
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 USA
| | - A. Salnikov
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 USA
| | - D. Schneider
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 USA
| | - T. Tookey
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 USA
| | - M. Weaver
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 USA
| | - C. H. Yoon
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 USA
| | - A. Perazzo
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 USA
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42
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van Driel TB, Kjær KS, Hartsock RW, Dohn AO, Harlang T, Chollet M, Christensen M, Gawelda W, Henriksen NE, Kim JG, Haldrup K, Kim KH, Ihee H, Kim J, Lemke H, Sun Z, Sundström V, Zhang W, Zhu D, Møller KB, Nielsen MM, Gaffney KJ. Atomistic characterization of the active-site solvation dynamics of a model photocatalyst. Nat Commun 2016; 7:13678. [PMID: 27892472 PMCID: PMC5133712 DOI: 10.1038/ncomms13678] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 10/25/2016] [Indexed: 12/22/2022] Open
Abstract
The interactions between the reactive excited state of molecular photocatalysts and surrounding solvent dictate reaction mechanisms and pathways, but are not readily accessible to conventional optical spectroscopic techniques. Here we report an investigation of the structural and solvation dynamics following excitation of a model photocatalytic molecular system [Ir2(dimen)4]2+, where dimen is para-diisocyanomenthane. The time-dependent structural changes in this model photocatalyst, as well as the changes in the solvation shell structure, have been measured with ultrafast diffuse X-ray scattering and simulated with Born-Oppenheimer Molecular Dynamics. Both methods provide direct access to the solute–solvent pair distribution function, enabling the solvation dynamics around the catalytically active iridium sites to be robustly characterized. Our results provide evidence for the coordination of the iridium atoms by the acetonitrile solvent and demonstrate the viability of using diffuse X-ray scattering at free-electron laser sources for studying the dynamics of photocatalysis. Interactions between reactive excited states of molecular photocatalysts and surrounding solvent can dictate reaction pathways, but are not readily accessible to conventional spectroscopic methods. Here the authors use diffuse X-ray scattering and theory to study the atomistic solvation dynamics of a photoexcited di-iridium complex in acetonitrile.
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Affiliation(s)
- Tim B van Driel
- Molecular Movies, Department of Physics, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.,LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Kasper S Kjær
- Molecular Movies, Department of Physics, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.,PULSE Institute, SLAC National Accelerator Laboratory, Stanford University, Stanford, California 94305, USA.,Chemical Physics Department, PO Box 124, Lund University, S-22100 Lund, Sweden
| | - Robert W Hartsock
- PULSE Institute, SLAC National Accelerator Laboratory, Stanford University, Stanford, California 94305, USA
| | - Asmus O Dohn
- Department of Chemistry, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Tobias Harlang
- Molecular Movies, Department of Physics, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.,Chemical Physics Department, PO Box 124, Lund University, S-22100 Lund, Sweden
| | - Matthieu Chollet
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Morten Christensen
- Molecular Movies, Department of Physics, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Wojciech Gawelda
- European XFEL GmbH, Holzkoppel 4, D-22869 Schenefeld, Germany.,Institute of Physics, Jan Kochanowski University, 25-406 Kielce, Poland
| | - Niels E Henriksen
- Department of Chemistry, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Jong Goo Kim
- Department of Chemistry, KAIST, Daejeon 305-701, South Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science, Daejeon 305-701, South Korea
| | - Kristoffer Haldrup
- Molecular Movies, Department of Physics, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Kyung Hwan Kim
- Department of Chemistry, KAIST, Daejeon 305-701, South Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science, Daejeon 305-701, South Korea
| | - Hyotcherl Ihee
- Department of Chemistry, KAIST, Daejeon 305-701, South Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science, Daejeon 305-701, South Korea
| | - Jeongho Kim
- Department of Chemistry, Inha University, Incheon 402-751, South Korea
| | - Henrik Lemke
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Zheng Sun
- PULSE Institute, SLAC National Accelerator Laboratory, Stanford University, Stanford, California 94305, USA
| | - Villy Sundström
- Chemical Physics Department, PO Box 124, Lund University, S-22100 Lund, Sweden
| | - Wenkai Zhang
- PULSE Institute, SLAC National Accelerator Laboratory, Stanford University, Stanford, California 94305, USA
| | - Diling Zhu
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Klaus B Møller
- Department of Chemistry, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Martin M Nielsen
- Molecular Movies, Department of Physics, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Kelly J Gaffney
- PULSE Institute, SLAC National Accelerator Laboratory, Stanford University, Stanford, California 94305, USA
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43
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Selenium single-wavelength anomalous diffraction de novo phasing using an X-ray-free electron laser. Nat Commun 2016; 7:13388. [PMID: 27811937 PMCID: PMC5097167 DOI: 10.1038/ncomms13388] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 09/28/2016] [Indexed: 01/08/2023] Open
Abstract
Structural information about biological macromolecules near the atomic scale provides important insight into the functions of these molecules. To date, X-ray crystallography has been the predominant method used for macromolecular structure determination. However, challenges exist when solving structures with X-rays, including the phase problem and radiation damage. X-ray-free electron lasers (X-ray FELs) have enabled collection of diffraction information before the onset of radiation damage, yet the majority of structures solved at X-ray FELs have been phased using external information via molecular replacement. De novo phasing at X-ray FELs has proven challenging due in part to per-pulse variations in intensity and wavelength. Here we report the solution of a selenobiotinyl-streptavidin structure using phases obtained by the anomalous diffraction of selenium measured at a single wavelength (Se-SAD) at the Linac Coherent Light Source. Our results demonstrate Se-SAD, routinely employed at synchrotrons for novel structure determination, is now possible at X-ray FELs. X-ray free electron lasers are increasingly available for use in macromolecular structure determination. Here, the authors describe the successful use of selenium single-wavelength anomalous diffraction data to calculate experimentally derived phases.
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44
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Nagler B, Schropp A, Galtier EC, Arnold B, Brown SB, Fry A, Gleason A, Granados E, Hashim A, Hastings JB, Samberg D, Seiboth F, Tavella F, Xing Z, Lee HJ, Schroer CG. The phase-contrast imaging instrument at the matter in extreme conditions endstation at LCLS. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2016; 87:103701. [PMID: 27802688 DOI: 10.1063/1.4963906] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 09/20/2016] [Indexed: 06/06/2023]
Abstract
We describe the phase-contrast imaging instrument at the Matter in Extreme Conditions (MEC) endstation of the Linac Coherent Light Source. The instrument can image phenomena with a spatial resolution of a few hundreds of nanometers and at the same time reveal the atomic structure through X-ray diffraction, with a temporal resolution better than 100 fs. It was specifically designed for studies relevant to high-energy-density science and can monitor, e.g., shock fronts, phase transitions, or void collapses. This versatile instrument was commissioned last year and is now available to the MEC user community.
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Affiliation(s)
- Bob Nagler
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Andreas Schropp
- Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, D-22607 Hamburg, Germany
| | - Eric C Galtier
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Brice Arnold
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Shaughnessy B Brown
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Alan Fry
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Arianna Gleason
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Eduardo Granados
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Akel Hashim
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Jerome B Hastings
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Dirk Samberg
- Institute of Structural Physics, Technische Universität Dresden, 01062 Dresden, Germany
| | - Frank Seiboth
- Institute of Structural Physics, Technische Universität Dresden, 01062 Dresden, Germany
| | - Franz Tavella
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Zhou Xing
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Hae Ja Lee
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Christian G Schroer
- Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, D-22607 Hamburg, Germany
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45
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Batyuk A, Galli L, Ishchenko A, Han GW, Gati C, Popov PA, Lee MY, Stauch B, White TA, Barty A, Aquila A, Hunter MS, Liang M, Boutet S, Pu M, Liu ZJ, Nelson G, James D, Li C, Zhao Y, Spence JCH, Liu W, Fromme P, Katritch V, Weierstall U, Stevens RC, Cherezov V. Native phasing of x-ray free-electron laser data for a G protein-coupled receptor. SCIENCE ADVANCES 2016; 2:e1600292. [PMID: 27679816 PMCID: PMC5035125 DOI: 10.1126/sciadv.1600292] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 08/01/2016] [Indexed: 05/23/2023]
Abstract
Serial femtosecond crystallography (SFX) takes advantage of extremely bright and ultrashort pulses produced by x-ray free-electron lasers (XFELs), allowing for the collection of high-resolution diffraction intensities from micrometer-sized crystals at room temperature with minimal radiation damage, using the principle of "diffraction-before-destruction." However, de novo structure factor phase determination using XFELs has been difficult so far. We demonstrate the ability to solve the crystallographic phase problem for SFX data collected with an XFEL using the anomalous signal from native sulfur atoms, leading to a bias-free room temperature structure of the human A2A adenosine receptor at 1.9 Å resolution. The advancement was made possible by recent improvements in SFX data analysis and the design of injectors and delivery media for streaming hydrated microcrystals. This general method should accelerate structural studies of novel difficult-to-crystallize macromolecules and their complexes.
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Affiliation(s)
- Alexander Batyuk
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Lorenzo Galli
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Andrii Ishchenko
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA.; Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA
| | - Gye Won Han
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA.; Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA
| | - Cornelius Gati
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Petr A Popov
- Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA.; Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia.; Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Ming-Yue Lee
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA.; Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA
| | - Benjamin Stauch
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA.; Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA
| | - Thomas A White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Andrew Aquila
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Mengning Liang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Mengchen Pu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhi-Jie Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.; iHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Garrett Nelson
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Daniel James
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Chufeng Li
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Yun Zhao
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - John C H Spence
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Wei Liu
- Center for Applied Structural Discovery at the Biodesign Institute, School of Molecular Sciences, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
| | - Petra Fromme
- Center for Applied Structural Discovery at the Biodesign Institute, School of Molecular Sciences, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
| | - Vsevolod Katritch
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA.; Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA.; Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Uwe Weierstall
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Raymond C Stevens
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA.; Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA.; Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.; iHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Vadim Cherezov
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA.; Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA.; Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia.; Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.; Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA
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46
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Sikorski M, Feng Y, Song S, Zhu D, Carini G, Herrmann S, Nishimura K, Hart P, Robert A. Application of an ePix100 detector for coherent scattering using a hard X-ray free-electron laser. JOURNAL OF SYNCHROTRON RADIATION 2016; 23:1171-1179. [PMID: 27577772 DOI: 10.1107/s1600577516010869] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 07/05/2016] [Indexed: 06/06/2023]
Abstract
A prototype ePix100 detector was used in small-angle scattering geometry to capture speckle patterns from a static sample using the Linac Coherent Light Source (LCLS) hard X-ray free-electron laser at 8.34 keV. The average number of detected photons per pixel per pulse was varied over three orders of magnitude from about 23 down to 0.01 to test the detector performance. At high average photon count rates, the speckle contrast was evaluated by analyzing the probability distribution of the pixel counts at a constant scattering vector for single frames. For very low average photon counts of less than 0.2 per pixel, the `droplet algorithm' was first applied to the patterns for correcting the effect of charge sharing, and then the pixel count statistics of multiple frames were analyzed collectively to extract the speckle contrast. Results obtained using both methods agree within the uncertainty intervals, providing strong experimental evidence for the validity of the statistical analysis. More importantly it confirms the suitability of the ePix100 detector for X-ray coherent scattering experiments, especially at very low count rates with performances surpassing those of previously available LCLS detectors.
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Affiliation(s)
- Marcin Sikorski
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Yiping Feng
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Sanghoon Song
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Diling Zhu
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Gabriella Carini
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Sven Herrmann
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Kurtis Nishimura
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Philip Hart
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Aymeric Robert
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
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47
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Thayer J, Damiani D, Ford C, Gaponenko I, Kroeger W, O'Grady C, Pines J, Tookey T, Weaver M, Perazzo A. Data systems for the Linac Coherent Light Source. J Appl Crystallogr 2016. [DOI: 10.1107/s1600576716011055] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The data acquisition and data management systems for X-ray free-electron laser experiments at the Linac Coherent Light Source are described. These systems are designed to acquire and to reliably transport shot-by-shot data at a peak throughput of 5 GB s−1to the offline data storage, where experimental data and the relevant metadata are archived and made available for user analysis. A case study of a serial femtosecond crystallography pipeline is presented.
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48
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Lyubimov AY, Uervirojnangkoorn M, Zeldin OB, Brewster AS, Murray TD, Sauter NK, Berger JM, Weis WI, Brunger AT. IOTA: integration optimization, triage and analysis tool for the processing of XFEL diffraction images. J Appl Crystallogr 2016; 49:1057-1064. [PMID: 27275148 PMCID: PMC4886991 DOI: 10.1107/s1600576716006683] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 04/19/2016] [Indexed: 01/25/2023] Open
Abstract
Serial femtosecond crystallography (SFX) uses an X-ray free-electron laser to extract diffraction data from crystals not amenable to conventional X-ray light sources owing to their small size or radiation sensitivity. However, a limitation of SFX is the high variability of the diffraction images that are obtained. As a result, it is often difficult to determine optimal indexing and integration parameters for the individual diffraction images. Presented here is a software package, called IOTA, which uses a grid-search technique to determine optimal spot-finding parameters that can in turn affect the success of indexing and the quality of integration on an image-by-image basis. Integration results can be filtered using a priori information about the Bravais lattice and unit-cell dimensions and analyzed for unit-cell isomorphism, facilitating an improvement in subsequent data-processing steps.
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Affiliation(s)
- Artem Y. Lyubimov
- Department of Molecular and Cellular Physiology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Monarin Uervirojnangkoorn
- Department of Molecular and Cellular Physiology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Oliver B. Zeldin
- Department of Molecular and Cellular Physiology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Aaron S. Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Thomas D. Murray
- Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - James M. Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - William I. Weis
- Department of Molecular and Cellular Physiology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
| | - Axel T. Brunger
- Department of Molecular and Cellular Physiology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
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49
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Zhou XE, Gao X, Barty A, Kang Y, He Y, Liu W, Ishchenko A, White TA, Yefanov O, Han GW, Xu Q, de Waal PW, Suino-Powell KM, Boutet S, Williams GJ, Wang M, Li D, Caffrey M, Chapman HN, Spence JCH, Fromme P, Weierstall U, Stevens RC, Cherezov V, Melcher K, Xu HE. X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex. Sci Data 2016; 3:160021. [PMID: 27070998 PMCID: PMC4828943 DOI: 10.1038/sdata.2016.21] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 02/25/2016] [Indexed: 01/01/2023] Open
Abstract
Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.
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Affiliation(s)
- X Edward Zhou
- Laboratory of Structural Sciences, Center for Structural Biology and Drug Discovery, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
| | - Xiang Gao
- Laboratory of Structural Sciences, Center for Structural Biology and Drug Discovery, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
| | - Anton Barty
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Yanyong Kang
- Laboratory of Structural Sciences, Center for Structural Biology and Drug Discovery, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
| | - Yuanzheng He
- Laboratory of Structural Sciences, Center for Structural Biology and Drug Discovery, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
| | - Wei Liu
- School of Molecular Sciences, and Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona 85287-1604, USA
| | - Andrii Ishchenko
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, California 90089, USA
| | - Thomas A White
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Gye Won Han
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, California 90089, USA.,Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, California 90089, USA
| | - Qingping Xu
- Joint Center for Structural Genomics, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Parker W de Waal
- Laboratory of Structural Sciences, Center for Structural Biology and Drug Discovery, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
| | - Kelly M Suino-Powell
- Laboratory of Structural Sciences, Center for Structural Biology and Drug Discovery, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
| | - Sébastien Boutet
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Garth J Williams
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Meitian Wang
- Swiss Light Source at Paul Scherrer Institute, CH-5232 Villigen, Switzerland
| | - Dianfan Li
- School of Medicine and School of Biochemistry and Immunology, Trinity College, Dublin D02 R590, Ireland
| | - Martin Caffrey
- School of Medicine and School of Biochemistry and Immunology, Trinity College, Dublin D02 R590, Ireland
| | - Henry N Chapman
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany.,Centre for Ultrafast Imaging, 22761 Hamburg, Germany
| | - John C H Spence
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany.,Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
| | - Petra Fromme
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Uwe Weierstall
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany.,Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
| | - Raymond C Stevens
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, California 90089, USA.,Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, California 90089, USA.,iHuman Institute, Shanghai Tech University, 2F Building 6, 99 Haike Road, Pudong New District, Shanghai 201210, China
| | - Vadim Cherezov
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, California 90089, USA
| | - Karsten Melcher
- Laboratory of Structural Sciences, Center for Structural Biology and Drug Discovery, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
| | - H Eric Xu
- Laboratory of Structural Sciences, Center for Structural Biology and Drug Discovery, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA.,VARI-SIMM Center, Center for Structure and Function of Drug Targets, CAS-Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
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50
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White WE, Robert A, Dunne M. The Linac Coherent Light Source. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:472-6. [PMID: 25931055 PMCID: PMC4416663 DOI: 10.1107/s1600577515005196] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 03/13/2015] [Indexed: 05/29/2023]
Abstract
The Linac Coherent Light Source (LCLS) at the SLAC National Accelerator Laboratory was the first hard X-ray free-electron laser (FEL) to operate as a user facility. After five years of operation, LCLS is now a mature FEL user facility. Our personal views about opportunities and challenges inherent to these unique light sources are discussed.
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Affiliation(s)
- William E. White
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Aymeric Robert
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Mike Dunne
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
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