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Banerjee S, Jurek Z, Abdullah MM, Santra R. Chemical effects on the dynamics of organic molecules irradiated with high intensity x rays. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2022; 9:054101. [PMID: 36329869 PMCID: PMC9625838 DOI: 10.1063/4.0000166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
The interaction of a high intensity x-ray pulse with matter causes ionization of the constituent atoms through various atomic processes, and the system eventually goes through a complex structural dynamics. Understanding this whole process is important from the perspective of structure determination of molecules using single particle imaging. XMDYN, which is a classical molecular dynamics-Monte Carlo based hybrid approach, has been successful in simulating the dynamical evolution of various systems under intense irradiation over the past years. The present study aims for extending the XMDYN toolkit to treat chemical bonds using the reactive force field. In order to study its impact, a highly intense x-ray pulse was made to interact with the simplest amino acid, glycine. Different model variants were used to highlight the consequences of charge rearrangement and chemical bonds on the time evolution. The charge-rearrangement-enhanced x-ray ionization of molecules effect is also discussed to address the capability of a classical MD based approach, i.e., XMDYN, to capture such a molecular phenomenon.
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Affiliation(s)
- Sourav Banerjee
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen-Synchrotron (DESY), Notkestr. 85, 22607 Hamburg, Germany
| | - Zoltan Jurek
- Authors to whom correspondence should be addressed: and
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Lipp V, Milov I, Medvedev N. Quantifying electron cascade size in various irradiated materials for free-electron laser applications. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:323-330. [PMID: 35254294 PMCID: PMC8900838 DOI: 10.1107/s1600577522000339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Studying electron- and X-ray-induced electron cascades in solids is essential for various research areas at free-electron laser facilities, such as X-ray imaging, crystallography, pulse diagnostics or X-ray-induced damage. To better understand the fundamental factors that define the duration and spatial size of such cascades, this work investigates the electron propagation in ten solids relevant for the applications of X-ray lasers: Au, B4C, diamond, Ni, polystyrene, Ru, Si, SiC, Si3N4 and W. Using classical Monte Carlo simulation in the atomic approximation, we study the dependence of the cascade size on the incident electron or photon energy and on the target parameters. The results show that an electron-induced cascade is systematically larger than a photon-induced cascade. Moreover, in contrast with the common assumption, the maximal cascade size does not necessarily coincide with the electron range. It was found that the cascade size can be controlled by careful selection of the photon energy for a particular material. Photon energy, just above an ionization potential, can essentially split the absorbed energy between two electrons (photo- and Auger), reducing their initial energy and thus shrinking the cascade size. This analysis suggests a way of tailoring the electron cascades for applications requiring either small cascades with a high density of excited electrons or large-spread cascades with lower electron densities.
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Affiliation(s)
- Vladimir Lipp
- Institute of Nuclear Physics, Polish Academy of Sciences, Radzikowskiego 152, 31-342 Kraków, Poland
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Igor Milov
- Industrial Focus Group XUV Optics, MESA+ Institute for Nanotechnology, University of Twente, Drienerlolaan 5, 7522 NB Enschede, The Netherlands
| | - Nikita Medvedev
- Institute of Physics, Czech Academy of Sciences, Na Slovance 2, 18221 Prague 8, Czech Republic
- Institute of Plasma Physics, Czech Academy of Sciences, Za Slovankou 3, 18200 Prague 8, Czech Republic
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Lovelace JJ, Borgstahl GEO. Characterizing pathological imperfections in macromolecular crystals: lattice disorders and modulations. CRYSTALLOGR REV 2019; 26:3-50. [PMID: 33041501 DOI: 10.1080/0889311x.2019.1692341] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Jeffrey J Lovelace
- The Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, 68198-6805, USA
| | - Gloria E O Borgstahl
- The Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, 68198-6805, USA
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Nass K. Radiation damage in protein crystallography at X-ray free-electron lasers. Acta Crystallogr D Struct Biol 2019; 75:211-218. [PMID: 30821709 PMCID: PMC6400258 DOI: 10.1107/s2059798319000317] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 01/07/2019] [Indexed: 01/17/2023] Open
Abstract
Radiation damage is still the most limiting factor in obtaining high-resolution structures of macromolecules in crystallographic experiments at synchrotrons. With the advent of X-ray free-electron lasers (XFELs) that produce ultrashort and highly intense X-ray pulses, it became possible to outrun most of the radiation-damage processes occurring in the sample during exposure to XFEL radiation. Although this is generally the case, several experimental and theoretical studies have indicated that structures from XFELs may not always be radiation-damage free. This is especially true when higher intensity pulses are used and protein molecules that contain heavy elements in their structures are studied. Here, the radiation-damage mechanisms that occur in samples exposed to XFEL pulses are summarized, results that show indications of radiation damage are reviewed and methods that can partially overcome it are discussed.
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Affiliation(s)
- Karol Nass
- Swiss Light Source, Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen, Switzerland
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Awel S, Kirian RA, Wiedorn MO, Beyerlein KR, Roth N, Horke DA, Oberthür D, Knoska J, Mariani V, Morgan A, Adriano L, Tolstikova A, Xavier PL, Yefanov O, Aquila A, Barty A, Roy-Chowdhury S, Hunter MS, James D, Robinson JS, Weierstall U, Rode AV, Bajt S, Küpper J, Chapman HN. Femtosecond X-ray diffraction from an aerosolized beam of protein nanocrystals. J Appl Crystallogr 2018; 51:133-139. [PMID: 29507547 PMCID: PMC5822990 DOI: 10.1107/s1600576717018131] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 12/19/2017] [Indexed: 11/10/2022] Open
Abstract
High-resolution Bragg diffraction from aerosolized single granulovirus nanocrystals using an X-ray free-electron laser is demonstrated. The outer dimensions of the in-vacuum aerosol injector components are identical to conventional liquid-microjet nozzles used in serial diffraction experiments, which allows the injector to be utilized with standard mountings. As compared with liquid-jet injection, the X-ray scattering background is reduced by several orders of magnitude by the use of helium carrier gas rather than liquid. Such reduction is required for diffraction measurements of small macromolecular nanocrystals and single particles. High particle speeds are achieved, making the approach suitable for use at upcoming high-repetition-rate facilities.
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Affiliation(s)
- Salah Awel
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | | | - Max O. Wiedorn
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Kenneth R. Beyerlein
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Nils Roth
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Daniel A. Horke
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Dominik Oberthür
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Juraj Knoska
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Valerio Mariani
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Andrew Morgan
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Luigi Adriano
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Alexandra Tolstikova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - P. Lourdu Xavier
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Max-Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Andrew Aquila
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Mark S. Hunter
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | | | - Joseph S. Robinson
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | | | - Andrei V. Rode
- Laser Physics Centre, Research School of Physics and Engineering, Australian National University, ACT 2601, Canberra, Australia
| | - Saša Bajt
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Jochen Küpper
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Henry N. Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
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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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Helliwell JR. New developments in crystallography: exploring its technology, methods and scope in the molecular biosciences. Biosci Rep 2017; 37:BSR20170204. [PMID: 28572170 PMCID: PMC6434086 DOI: 10.1042/bsr20170204] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 05/31/2017] [Accepted: 06/01/2017] [Indexed: 12/16/2022] Open
Abstract
Since the Protein Data Bank (PDB) was founded in 1971, there are now over 120,000 depositions, the majority of which are from X-ray crystallography and 90% of those made use of synchrotron beamlines. At the Cambridge Structure Database (CSD), founded in 1965, there are more than 800,000 'small molecule' crystal structure depositions and a very large number of those are relevant in the biosciences as ligands or cofactors. The technology for crystal structure analysis is still developing rapidly both at synchrotrons and in home labs. Determination of the details of the hydrogen atoms in biological macromolecules is well served using neutrons as probe. Large multi-macromolecular complexes cause major challenges to crystallization; electrons as probes offer unique advantages here. Methods developments naturally accompany technology change, mainly incremental but some, such as the tuneability, intensity and collimation of synchrotron radiation, have effected radical changes in capability of biological crystallography. In the past few years, the X-ray laser has taken X-ray crystallography measurement times into the femtosecond range. In terms of applications many new discoveries have been made in the molecular biosciences. The scope of crystallographic techniques is indeed very wide. As examples, new insights into chemical catalysis of enzymes and relating ligand bound structures to thermodynamics have been gained but predictive power is seen as not yet achieved. Metal complexes are also an emerging theme for biomedicine applications. Our studies of coloration of live and cooked lobsters proved to be an unexpected favourite with the public and schoolchildren. More generally, public understanding of the biosciences and crystallography's role within the field have been greatly enhanced by the United Nations International Year of Crystallography coordinated by the International Union of Crystallography. This topical review describes each of these areas along with illustrative results to document the scope of each methodology.
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Casaretto N, Schaniel D, Alle P, Wenger E, Parois P, Fournier B, Bendeif EE, Palin C, Pillet S. In-house time-resolved photocrystallography on the millisecond timescale using a gated X-ray hybrid pixel area detector. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2017; 73:696-707. [PMID: 28762979 DOI: 10.1107/s2052520617009234] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 06/19/2017] [Indexed: 11/10/2022]
Abstract
With the remarkable progress of accelerator-based X-ray sources in terms of intensity and brightness, the investigation of structural dynamics from time-resolved X-ray diffraction methods is becoming widespread in chemistry, biochemistry and materials science applications. Diffraction patterns can now be measured down to the femtosecond time-scale using X-ray free electron lasers or table-top laser plasma X-ray sources. On the other hand, the recent developments in photon counting X-ray area detectors offer new opportunities for time-resolved crystallography. Taking advantage of the fast read-out, the internal stacking of recorded images, and the gating possibilities (electronic shutter) of the XPAD hybrid pixel detector, we implemented a laboratory X-ray diffractometer for time-resolved single-crystal X-ray diffraction after pulsed laser excitation, combined with transient optical absorption measurement. The experimental method and instrumental setup are described in detail, and validated using the photoinduced nitrosyl linkage isomerism of sodium nitroprusside, Na2[Fe(CN)5NO]·2H2O, as proof of principle. Light-induced Bragg intensity relative variations ΔI(hkl)/I(hkl) of the order of 1%, due to the photoswitching of the NO ligand, could be detected with a 6 ms acquisition window. The capabilities of such a laboratory time-resolved experiment are critically evaluated.
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Affiliation(s)
- Nicolas Casaretto
- CRM2, UMR 7036, Université de Lorraine, 54506 Vandoeuvre-les-Nancy, France
| | - Dominik Schaniel
- CRM2, UMR 7036, Université de Lorraine, 54506 Vandoeuvre-les-Nancy, France
| | - Paul Alle
- CRM2, UMR 7036, Université de Lorraine, 54506 Vandoeuvre-les-Nancy, France
| | - Emmanuel Wenger
- CRM2, UMR 7036, Université de Lorraine, 54506 Vandoeuvre-les-Nancy, France
| | - Pascal Parois
- CRM2, UMR 7036, Université de Lorraine, 54506 Vandoeuvre-les-Nancy, France
| | - Bertrand Fournier
- CRM2, UMR 7036, Université de Lorraine, 54506 Vandoeuvre-les-Nancy, France
| | - El Eulmi Bendeif
- CRM2, UMR 7036, Université de Lorraine, 54506 Vandoeuvre-les-Nancy, France
| | - Cyril Palin
- CRM2, UMR 7036, Université de Lorraine, 54506 Vandoeuvre-les-Nancy, France
| | - Sébastien Pillet
- CRM2, UMR 7036, Université de Lorraine, 54506 Vandoeuvre-les-Nancy, France
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9
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Spectroscopy and Chemical Bonding in Transition Metal Complexes. STRUCTURE AND BONDING 2016. [DOI: 10.1007/430_2015_195] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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10
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Aranda MA. Recent studies of cements and concretes by synchrotron radiation crystallographic and cognate methods. CRYSTALLOGR REV 2015. [DOI: 10.1080/0889311x.2015.1070260] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Wu W, Yan C, Shi X, Li L, Liu W, Xu C. Lipid in T-cell receptor transmembrane signaling. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 118:130-8. [DOI: 10.1016/j.pbiomolbio.2015.04.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Revised: 04/20/2015] [Accepted: 04/22/2015] [Indexed: 12/18/2022]
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Hao Y, Inhester L, Hanasaki K, Son SK, Santra R. Efficient electronic structure calculation for molecular ionization dynamics at high x-ray intensity. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:041707. [PMID: 26798806 PMCID: PMC4711638 DOI: 10.1063/1.4919794] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 04/24/2015] [Indexed: 05/16/2023]
Abstract
We present the implementation of an electronic-structure approach dedicated to ionization dynamics of molecules interacting with x-ray free-electron laser (XFEL) pulses. In our scheme, molecular orbitals for molecular core-hole states are represented by linear combination of numerical atomic orbitals that are solutions of corresponding atomic core-hole states. We demonstrate that our scheme efficiently calculates all possible multiple-hole configurations of molecules formed during XFEL pulses. The present method is suitable to investigate x-ray multiphoton multiple ionization dynamics and accompanying nuclear dynamics, providing essential information on the chemical dynamics relevant for high-intensity x-ray imaging.
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Schlichting I. Serial femtosecond crystallography: the first five years. IUCRJ 2015; 2:246-55. [PMID: 25866661 PMCID: PMC4392417 DOI: 10.1107/s205225251402702x] [Citation(s) in RCA: 225] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 12/09/2014] [Indexed: 05/18/2023]
Abstract
Protein crystallography using synchrotron radiation sources has had a tremendous impact on biology, having yielded the structures of thousands of proteins and given detailed insight into their mechanisms. However, the technique is limited by the requirement for macroscopic crystals, which can be difficult to obtain, as well as by the often severe radiation damage caused in diffraction experiments, in particular when using tiny crystals. To slow radiation damage, data collection is typically performed at cryogenic temperatures. With the advent of free-electron lasers (FELs) capable of delivering extremely intense femtosecond X-ray pulses, this situation appears to be remedied, allowing the structure determination of undamaged macromolecules using either macroscopic or microscopic crystals. The latter are exposed to the FEL beam in random orientations and their diffraction data are collected at cryogenic or room temperature in a serial fashion, since each crystal is destroyed upon a single exposure. The new approaches required for crystal growth and delivery, and for diffraction data analysis, including de novo phasing, are reviewed. The opportunities and challenges of SFX are described, including applications such as time-resolved measurements and the analysis of radiation damage-prone systems.
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Affiliation(s)
- Ilme Schlichting
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, Heidelberg 69120, Germany
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