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Mobley BR, Schmidt KE, Chen JPJ, Kirian RA. A Metropolis Monte Carlo algorithm for merging single-particle diffraction intensities. Acta Crystallogr A Found Adv 2022; 78:200-211. [DOI: 10.1107/s2053273322001395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 02/04/2022] [Indexed: 11/10/2022]
Abstract
Single-particle imaging with X-ray free-electron lasers depends crucially on algorithms that merge large numbers of weak diffraction patterns despite missing measurements of parameters such as particle orientations. The expand–maximize–compress (EMC) algorithm is highly effective at merging single-particle diffraction patterns with missing orientation values, but most implementations exhaustively sample the space of missing parameters and may become computationally prohibitive as the number of degrees of freedom extends beyond orientation angles. This paper describes how the EMC algorithm can be modified to employ Metropolis Monte Carlo sampling rather than grid sampling, which may be favorable for reconstruction problems with more than three missing parameters. Using simulated data, this variant is compared with the standard EMC algorithm.
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Chen JPJ, Donatelli JJ, Schmidt KE, Kirian RA. Shape transform phasing of edgy nanocrystals. Acta Crystallogr A Found Adv 2019; 75:239-259. [PMID: 30821258 DOI: 10.1107/s205327331900113x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 01/22/2019] [Indexed: 11/11/2022]
Abstract
Diffraction patterns from small protein crystals illuminated by highly coherent X-rays often contain measurable interference signals between Bragg peaks. This coherent `shape transform' signal introduces enough additional information to allow the molecular densities to be determined from the diffracted intensities directly, without prior information or resolution restrictions. However, the various correlations amongst molecular occupancies/vacancies at the crystal surface result in a subtle yet critical problem in shape transform phasing whereby the sublattices of symmetry-related molecules exhibit a form of partial coherence amongst lattice sites when an average is taken over many crystal patterns. Here an iterative phase retrieval algorithm is developed which is capable of treating this problem; it is demonstrated on simulated data.
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Affiliation(s)
- J P J Chen
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - J J Donatelli
- Center for Advanced Mathematics for Energy Research Applications, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - K E Schmidt
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - R A Kirian
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
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Kirian RA, Awel S, Eckerskorn N, Fleckenstein H, Wiedorn M, Adriano L, Bajt S, Barthelmess M, Bean R, Beyerlein KR, Chavas LMG, Domaracky M, Heymann M, Horke DA, Knoska J, Metz M, Morgan A, Oberthuer D, Roth N, Sato T, Xavier PL, Yefanov O, Rode AV, Küpper J, Chapman HN. Simple convergent-nozzle aerosol injector for single-particle diffractive imaging with X-ray free-electron lasers. Struct Dyn 2015; 2:041717. [PMID: 26798816 PMCID: PMC4711644 DOI: 10.1063/1.4922648] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 05/18/2015] [Indexed: 05/06/2023]
Abstract
A major challenge in high-resolution x-ray free-electron laser-based coherent diffractive imaging is the development of aerosol injectors that can efficiently deliver particles to the peak intensity of the focused X-ray beam. Here, we consider the use of a simple convergent-orifice nozzle for producing tightly focused beams of particles. Through optical imaging we show that 0.5 μm particles can be focused to a full-width at half maximum diameter of 4.2 μm, and we demonstrate the use of such a nozzle for injecting viruses into a micro-focused soft-X-ray FEL beam.
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Affiliation(s)
| | | | - N Eckerskorn
- Laser Physics Centre, Research School of Physics and Engineering, Australian National University , Canberra, Australia
| | - H Fleckenstein
- Center for Free-Electron Laser Science , DESY, 22607 Hamburg, Germany
| | | | - L Adriano
- Deutsches Elektronen-Synchrotron DESY , 22607 Hamburg, Germany
| | - S Bajt
- Deutsches Elektronen-Synchrotron DESY , 22607 Hamburg, Germany
| | - M Barthelmess
- Center for Free-Electron Laser Science , DESY, 22607 Hamburg, Germany
| | - R Bean
- European XFEL GmbH , 22761 Hamburg, Germany
| | - K R Beyerlein
- Center for Free-Electron Laser Science , DESY, 22607 Hamburg, Germany
| | - L M G Chavas
- Center for Free-Electron Laser Science , DESY, 22607 Hamburg, Germany
| | | | - M Heymann
- Center for Free-Electron Laser Science , DESY, 22607 Hamburg, Germany
| | - D A Horke
- Center for Free-Electron Laser Science , DESY, 22607 Hamburg, Germany
| | | | | | - A Morgan
- Center for Free-Electron Laser Science , DESY, 22607 Hamburg, Germany
| | - D Oberthuer
- Center for Free-Electron Laser Science , DESY, 22607 Hamburg, Germany
| | - N Roth
- Center for Free-Electron Laser Science , DESY, 22607 Hamburg, Germany
| | - T Sato
- Center for Free-Electron Laser Science , DESY, 22607 Hamburg, Germany
| | | | - O Yefanov
- Center for Free-Electron Laser Science , DESY, 22607 Hamburg, Germany
| | - A V Rode
- Laser Physics Centre, Research School of Physics and Engineering, Australian National University , Canberra, Australia
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Galli L, Son SK, Klinge M, Bajt S, Barty A, Bean R, Betzel C, Beyerlein KR, Caleman C, Doak RB, Duszenko M, Fleckenstein H, Gati C, Hunt B, Kirian RA, Liang M, Nanao MH, Nass K, Oberthür D, Redecke L, Shoeman R, Stellato F, Yoon CH, White TA, Yefanov O, Spence J, Chapman HN. Electronic damage in S atoms in a native protein crystal induced by an intense X-ray free-electron laser pulse. Struct Dyn 2015; 2:041703. [PMID: 26798803 PMCID: PMC4711609 DOI: 10.1063/1.4919398] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 04/17/2015] [Indexed: 05/07/2023]
Abstract
Current hard X-ray free-electron laser (XFEL) sources can deliver doses to biological macromolecules well exceeding 1 GGy, in timescales of a few tens of femtoseconds. During the pulse, photoionization can reach the point of saturation in which certain atomic species in the sample lose most of their electrons. This electronic radiation damage causes the atomic scattering factors to change, affecting, in particular, the heavy atoms, due to their higher photoabsorption cross sections. Here, it is shown that experimental serial femtosecond crystallography data collected with an extremely bright XFEL source exhibit a reduction of the effective scattering power of the sulfur atoms in a native protein. Quantitative methods are developed to retrieve information on the effective ionization of the damaged atomic species from experimental data, and the implications of utilizing new phasing methods which can take advantage of this localized radiation damage are discussed.
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Affiliation(s)
| | | | - M Klinge
- Joint Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University of Hamburg and Institute of Biochemistry, University of Luebeck at DESY, 22607 Hamburg, Germany
| | - S Bajt
- Photon Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
| | - A Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
| | - R Bean
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
| | - C Betzel
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, University of Hamburg at DESY, 22607 Hamburg, Germany
| | - K R Beyerlein
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
| | | | - R B Doak
- Department of Biomolecular Mechanisms, Max Planck-Institute for Medical Research , Jahnstrasse 29, 69120 Heidelberg, Germany
| | - M Duszenko
- Interfaculty Institute of Biochemistry, University of Tübingen , 72076 Tübingen, Germany
| | - H Fleckenstein
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
| | - C Gati
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
| | - B Hunt
- Department of Physics and Astronomy, Brigham Young University , Provo, Utah 84602, USA
| | - R A Kirian
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
| | - M Liang
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
| | - M H Nanao
- EMBL , Grenoble Outstation, Rue Jules Horowitz 6, Grenoble 38042, France
| | - K Nass
- Department of Biomolecular Mechanisms, Max Planck-Institute for Medical Research , Jahnstrasse 29, 69120 Heidelberg, Germany
| | - D Oberthür
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
| | - L Redecke
- Joint Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University of Hamburg and Institute of Biochemistry, University of Luebeck at DESY, 22607 Hamburg, Germany
| | - R Shoeman
- Department of Biomolecular Mechanisms, Max Planck-Institute for Medical Research , Jahnstrasse 29, 69120 Heidelberg, Germany
| | - F Stellato
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
| | | | - T A White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
| | - O Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
| | - J Spence
- Department of Physics, Arizona State University , Tempe, Arizona 85287-1504, USA
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Fromme P, Chapman H, Kupitz C, Hunter MS, Kirian RA, Barty A, White TA, Aquilla A, Stellato F, Beyerlein K, DePonte DP, Frank M, Schlichting I, Shoeman R, Lomb L, Steinbrenner J, Nass K, Boutet S, Bogan MJ, Williams G, Zatsepin N, Basu S, Wang D, James D, Fromme R, Grotjohann I, Bottin H, Cherezov V, Stevens R, Cobbe D, Cramer W, Stroud R, Doak RB, Weierstall U, Schmidt K, Spence JCH. Femtosecond nanocrystallography of membrane proteins opens a new era for structural biology. Acta Crystallogr A 2012. [DOI: 10.1107/s0108767312099461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Hunter MS, DePonte DP, Shapiro DA, Kirian RA, Wang X, Starodub D, Marchesini S, Weierstall U, Doak RB, Spence JCH, Fromme P. X-ray diffraction from membrane protein nanocrystals. Biophys J 2011; 100:198-206. [PMID: 21190672 DOI: 10.1016/j.bpj.2010.10.049] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Revised: 10/02/2010] [Accepted: 10/13/2010] [Indexed: 11/25/2022] Open
Abstract
Membrane proteins constitute > 30% of the proteins in an average cell, and yet the number of currently known structures of unique membrane proteins is < 300. To develop new concepts for membrane protein structure determination, we have explored the serial nanocrystallography method, in which fully hydrated protein nanocrystals are delivered to an x-ray beam within a liquid jet at room temperature. As a model system, we have collected x-ray powder diffraction data from the integral membrane protein Photosystem I, which consists of 36 subunits and 381 cofactors. Data were collected from crystals ranging in size from 100 nm to 2 μm. The results demonstrate that there are membrane protein crystals that contain < 100 unit cells (200 total molecules) and that 3D crystals of membrane proteins, which contain < 200 molecules, may be suitable for structural investigation. Serial nanocrystallography overcomes the problem of x-ray damage, which is currently one of the major limitations for x-ray structure determination of small crystals. By combining serial nanocrystallography with x-ray free-electron laser sources in the future, it may be possible to produce molecular-resolution electron-density maps using membrane protein crystals that contain only a few hundred or thousand unit cells.
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Affiliation(s)
- M S Hunter
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, USA
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Saldin DK, Poon HC, Bogan MJ, Marchesini S, Shapiro DA, Kirian RA, Weierstall U, Spence JCH. New light on disordered ensembles: ab initio structure determination of one particle from scattering fluctuations of many copies. Phys Rev Lett 2011; 106:115501. [PMID: 21469876 DOI: 10.1103/physrevlett.106.115501] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Indexed: 05/25/2023]
Abstract
We report on the first experimental ab initio reconstruction of an image of a single particle from fluctuations in the scattering from an ensemble of copies, randomly oriented about an axis. The method is applicable to identical particles frozen in space or time (as by snapshot diffraction from an x-ray free electron laser). These fluctuations enhance information obtainable from an experiment such as conventional small angle x-ray scattering.
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Affiliation(s)
- D K Saldin
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, USA
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