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Galli L, Son SK, Barends TRM, White TA, Barty A, Botha S, Boutet S, Caleman C, Doak RB, Nanao MH, Nass K, Shoeman RL, Timneanu N, Santra R, Schlichting I, Chapman HN. Towards phasing using high X-ray intensity. IUCRJ 2015; 2:627-34. [PMID: 26594370 PMCID: PMC4645107 DOI: 10.1107/s2052252515014049] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 07/24/2015] [Indexed: 05/11/2023]
Abstract
X-ray free-electron lasers (XFELs) show great promise for macromolecular structure determination from sub-micrometre-sized crystals, using the emerging method of serial femtosecond crystallography. The extreme brightness of the XFEL radiation can multiply ionize most, if not all, atoms in a protein, causing their scattering factors to change during the pulse, with a preferential 'bleaching' of heavy atoms. This paper investigates the effects of electronic damage on experimental data collected from a Gd derivative of lysozyme microcrystals at different X-ray intensities, and the degree of ionization of Gd atoms is quantified from phased difference Fourier maps. A pattern sorting scheme is proposed to maximize the ionization contrast and the way in which the local electronic damage can be used for a new experimental phasing method is discussed.
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Barends TRM, Foucar L, Ardevol A, Nass K, Aquila A, Botha S, Doak RB, Falahati K, Hartmann E, Hilpert M, Heinz M, Hoffmann MC, Köfinger J, Koglin JE, Kovacsova G, Liang M, Milathianaki D, Lemke HT, Reinstein J, Roome CM, Shoeman RL, Williams GJ, Burghardt I, Hummer G, Boutet S, Schlichting I. Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation. Science 2015; 350:445-50. [PMID: 26359336 DOI: 10.1126/science.aac5492] [Citation(s) in RCA: 268] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 08/26/2015] [Indexed: 11/02/2022]
Abstract
The hemoprotein myoglobin is a model system for the study of protein dynamics. We used time-resolved serial femtosecond crystallography at an x-ray free-electron laser to resolve the ultrafast structural changes in the carbonmonoxy myoglobin complex upon photolysis of the Fe-CO bond. Structural changes appear throughout the protein within 500 femtoseconds, with the C, F, and H helices moving away from the heme cofactor and the E and A helices moving toward it. These collective movements are predicted by hybrid quantum mechanics/molecular mechanics simulations. Together with the observed oscillations of residues contacting the heme, our calculations support the prediction that an immediate collective response of the protein occurs upon ligand dissociation, as a result of heme vibrational modes coupling to global modes of the protein.
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Bublitz M, Nass K, Drachmann ND, Markvardsen AJ, Gutmann MJ, Barends TRM, Mattle D, Shoeman RL, Doak RB, Boutet S, Messerschmidt M, Seibert MM, Williams GJ, Foucar L, Reinhard L, Sitsel O, Gregersen JL, Clausen JD, Boesen T, Gotfryd K, Wang KT, Olesen C, Møller JV, Nissen P, Schlichting I. Structural studies of P-type ATPase-ligand complexes using an X-ray free-electron laser. IUCRJ 2015; 2:409-20. [PMID: 26175901 PMCID: PMC4491313 DOI: 10.1107/s2052252515008969] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 05/08/2015] [Indexed: 05/24/2023]
Abstract
Membrane proteins are key players in biological systems, mediating signalling events and the specific transport of e.g. ions and metabolites. Consequently, membrane proteins are targeted by a large number of currently approved drugs. Understanding their functions and molecular mechanisms is greatly dependent on structural information, not least on complexes with functionally or medically important ligands. Structure determination, however, is hampered by the difficulty of obtaining well diffracting, macroscopic crystals. Here, the feasibility of X-ray free-electron-laser-based serial femtosecond crystallography (SFX) for the structure determination of membrane protein-ligand complexes using microcrystals of various native-source and recombinant P-type ATPase complexes is demonstrated. The data reveal the binding sites of a variety of ligands, including lipids and inhibitors such as the hallmark P-type ATPase inhibitor orthovanadate. By analyzing the resolution dependence of ligand densities and overall model qualities, SFX data quality metrics as well as suitable refinement procedures are discussed. Even at relatively low resolution and multiplicity, the identification of ligands can be demonstrated. This makes SFX a useful tool for ligand screening and thus for unravelling the molecular mechanisms of biologically active proteins.
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Barends T, White TA, Barty A, Foucar L, Messerschmidt M, Alonso-Mori R, Botha S, Chapman H, Doak RB, Galli L, Gati C, Gutmann M, Koglin J, Markvardsen A, Nass K, Oberthur D, Shoeman RL, Schlichting I, Boutet S. Effects of self-seeding and crystal post-selection on the quality of Monte Carlo-integrated SFX data. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:644-52. [PMID: 25931080 DOI: 10.1107/s1600577515005184] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 03/13/2015] [Indexed: 05/17/2023]
Abstract
Serial femtosecond crystallography (SFX) is an emerging method for data collection at free-electron lasers (FELs) in which single diffraction snapshots are taken from a large number of crystals. The partial intensities collected in this way are then combined in a scheme called Monte Carlo integration, which provides the full diffraction intensities. However, apart from having to perform this merging, the Monte Carlo integration must also average out all variations in crystal quality, crystal size, X-ray beam properties and other factors, necessitating data collection from thousands of crystals. Because the pulses provided by FELs running in the typical self-amplified spontaneous emission (SASE) mode of operation have very irregular, spiky spectra that vary strongly from pulse to pulse, it has been suggested that this is an important source of variation contributing to inaccuracies in the intensities, and that, by using monochromatic pulses produced through a process called self-seeding, fewer images might be needed for Monte Carlo integration to converge, resulting in more accurate data. This paper reports the results of two experiments performed at the Linac Coherent Light Source in which data collected in both SASE and self-seeded mode were compared. Importantly, no improvement attributable to the use of self-seeding was detected. In addition, other possible sources of variation that affect SFX data quality were investigated, such as crystal-to-crystal variations reflected in the unit-cell parameters; however, these factors were found to have no influence on data quality either. Possibly, there is another source of variation as yet undetected that affects SFX data quality much more than any of the factors investigated here.
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Boutet S, Foucar L, Barends TRM, Botha S, Doak RB, Koglin JE, Messerschmidt M, Nass K, Schlichting I, Seibert MM, Shoeman RL, Williams GJ. Characterization and use of the spent beam for serial operation of LCLS. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:634-43. [PMID: 25931079 PMCID: PMC4416680 DOI: 10.1107/s1600577515004002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 02/26/2015] [Indexed: 05/30/2023]
Abstract
X-ray free-electron laser sources such as the Linac Coherent Light Source offer very exciting possibilities for unique research. However, beam time at such facilities is very limited and in high demand. This has led to significant efforts towards beam multiplexing of various forms. One such effort involves re-using the so-called spent beam that passes through the hole in an area detector after a weak interaction with a primary sample. This beam can be refocused into a secondary interaction region and used for a second, independent experiment operating in series. The beam profile of this refocused beam was characterized for a particular experimental geometry at the Coherent X-ray Imaging instrument at LCLS. A demonstration of this multiplexing capability was performed with two simultaneous serial femtosecond crystallography experiments, both yielding interpretable data of sufficient quality to produce electron density maps.
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Nass K, Foucar L, Barends TRM, Hartmann E, Botha S, Shoeman RL, Doak RB, Alonso-Mori R, Aquila A, Bajt S, Barty A, Bean R, Beyerlein KR, Bublitz M, Drachmann N, Gregersen J, Jönsson HO, Kabsch W, Kassemeyer S, Koglin JE, Krumrey M, Mattle D, Messerschmidt M, Nissen P, Reinhard L, Sitsel O, Sokaras D, Williams GJ, Hau-Riege S, Timneanu N, Caleman C, Chapman HN, Boutet S, Schlichting I. Indications of radiation damage in ferredoxin microcrystals using high-intensity X-FEL beams. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:225-38. [PMID: 25723924 DOI: 10.1107/s1600577515002349] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 02/03/2015] [Indexed: 05/23/2023]
Abstract
Proteins that contain metal cofactors are expected to be highly radiation sensitive since the degree of X-ray absorption correlates with the presence of high-atomic-number elements and X-ray energy. To explore the effects of local damage in serial femtosecond crystallography (SFX), Clostridium ferredoxin was used as a model system. The protein contains two [4Fe-4S] clusters that serve as sensitive probes for radiation-induced electronic and structural changes. High-dose room-temperature SFX datasets were collected at the Linac Coherent Light Source of ferredoxin microcrystals. Difference electron density maps calculated from high-dose SFX and synchrotron data show peaks at the iron positions of the clusters, indicative of decrease of atomic scattering factors due to ionization. The electron density of the two [4Fe-4S] clusters differs in the FEL data, but not in the synchrotron data. Since the clusters differ in their detailed architecture, this observation is suggestive of an influence of the molecular bonding and geometry on the atomic displacement dynamics following initial photoionization. The experiments are complemented by plasma code calculations.
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Botha S, Nass K, Barends TRM, Kabsch W, Latz B, Dworkowski F, Foucar L, Panepucci E, Wang M, Shoeman RL, Schlichting I, Doak RB. Room-temperature serial crystallography at synchrotron X-ray sources using slowly flowing free-standing high-viscosity microstreams. ACTA ACUST UNITED AC 2015; 71:387-97. [DOI: 10.1107/s1399004714026327] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 11/30/2014] [Indexed: 11/10/2022]
Abstract
Recent advances in synchrotron sources, beamline optics and detectors are driving a renaissance in room-temperature data collection. The underlying impetus is the recognition that conformational differences are observed in functionally important regions of structures determined using crystals kept at ambient as opposed to cryogenic temperature during data collection. In addition, room-temperature measurements enable time-resolved studies and eliminate the need to find suitable cryoprotectants. Since radiation damage limits the high-resolution data that can be obtained from a single crystal, especially at room temperature, data are typically collected in a serial fashion using a number of crystals to spread the total dose over the entire ensemble. Several approaches have been developed over the years to efficiently exchange crystals for room-temperature data collection. These includein situcollection in trays, chips and capillary mounts. Here, the use of a slowly flowing microscopic stream for crystal delivery is demonstrated, resulting in extremely high-throughput delivery of crystals into the X-ray beam. This free-stream technology, which was originally developed for serial femtosecond crystallography at X-ray free-electron lasers, is here adapted to serial crystallography at synchrotrons. By embedding the crystals in a high-viscosity carrier stream, high-resolution room-temperature studies can be conducted at atmospheric pressure using the unattenuated X-ray beam, thus permitting the analysis of small or weakly scattering crystals. The high-viscosity extrusion injector is described, as is its use to collect high-resolution serial data from native and heavy-atom-derivatized lysozyme crystals at the Swiss Light Source using less than half a milligram of protein crystals. The room-temperature serial data allowde novostructure determination. The crystal size used in this proof-of-principle experiment was dictated by the available flux density. However, upcoming developments in beamline optics, detectors and synchrotron sources will enable the use of true microcrystals. This high-throughput, high-dose-rate methodology provides a new route to investigating the structure and dynamics of macromolecules at ambient temperature.
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Lee HH, Cherni I, Yu H, Fromme R, Doran JD, Grotjohann I, Mittman M, Basu S, Deb A, Dörner K, Aquila A, Barty A, Boutet S, Chapman HN, Doak RB, Hunter MS, James D, Kirian RA, Kupitz C, Lawrence RM, Liu H, Nass K, Schlichting I, Schmidt KE, Seibert MM, Shoeman RL, Spence JCH, Stellato F, Weierstall U, Williams GJ, Yoon C, Wang D, Zatsepin NA, Hogue BG, Matoba N, Fromme P, Mor TS. Expression, purification and crystallization of CTB-MPR, a candidate mucosal vaccine component against HIV-1. IUCRJ 2014; 1:305-17. [PMID: 25295172 PMCID: PMC4174873 DOI: 10.1107/s2052252514014900] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 06/24/2014] [Indexed: 05/03/2023]
Abstract
CTB-MPR is a fusion protein between the B subunit of cholera toxin (CTB) and the membrane-proximal region of gp41 (MPR), the transmembrane envelope protein of Human immunodeficiency virus 1 (HIV-1), and has previously been shown to induce the production of anti-HIV-1 antibodies with antiviral functions. To further improve the design of this candidate vaccine, X-ray crystallography experiments were performed to obtain structural information about this fusion protein. Several variants of CTB-MPR were designed, constructed and recombinantly expressed in Escherichia coli. The first variant contained a flexible GPGP linker between CTB and MPR, and yielded crystals that diffracted to a resolution of 2.3 Å, but only the CTB region was detected in the electron-density map. A second variant, in which the CTB was directly attached to MPR, was shown to destabilize pentamer formation. A third construct containing a polyalanine linker between CTB and MPR proved to stabilize the pentameric form of the protein during purification. The purification procedure was shown to produce a homogeneously pure and monodisperse sample for crystallization. Initial crystallization experiments led to pseudo-crystals which were ordered in only two dimensions and were disordered in the third dimension. Nanocrystals obtained using the same precipitant showed promising X-ray diffraction to 5 Å resolution in femtosecond nanocrystallography experiments at the Linac Coherent Light Source at the SLAC National Accelerator Laboratory. The results demonstrate the utility of femtosecond X-ray crystallography to enable structural analysis based on nano/microcrystals of a protein for which no macroscopic crystals ordered in three dimensions have been observed before.
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Arnlund D, Johansson LC, Wickstrand C, Barty A, Williams GJ, Malmerberg E, Davidsson J, Milathianaki D, DePonte DP, Shoeman RL, Wang D, James D, Katona G, Westenhoff S, White TA, Aquila A, Bari S, Berntsen P, Bogan M, van Driel TB, Doak RB, Kjær KS, Frank M, Fromme R, Grotjohann I, Henning R, Hunter MS, Kirian RA, Kosheleva I, Kupitz C, Liang M, Martin AV, Nielsen MM, Messerschmidt M, Seibert MM, Sjöhamn J, Stellato F, Weierstall U, Zatsepin NA, Spence JCH, Fromme P, Schlichting I, Boutet S, Groenhof G, Chapman HN, Neutze R. Visualizing a protein quake with time-resolved X-ray scattering at a free-electron laser. Nat Methods 2014; 11:923-6. [PMID: 25108686 DOI: 10.1038/nmeth.3067] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 07/09/2014] [Indexed: 01/07/2023]
Abstract
We describe a method to measure ultrafast protein structural changes using time-resolved wide-angle X-ray scattering at an X-ray free-electron laser. We demonstrated this approach using multiphoton excitation of the Blastochloris viridis photosynthetic reaction center, observing an ultrafast global conformational change that arises within picoseconds and precedes the propagation of heat through the protein. This provides direct structural evidence for a 'protein quake': the hypothesis that proteins rapidly dissipate energy through quake-like structural motions.
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35
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Johansson LC, Arnlund D, Katona G, White TA, Barty A, DePonte DP, Shoeman RL, Wickstrand C, Sharma A, Williams GJ, Aquila A, Bogan MJ, Caleman C, Davidsson J, Doak RB, Frank M, Fromme R, Galli L, Grotjohann I, Hunter MS, Kassemeyer S, Kirian RA, Kupitz C, Liang M, Lomb L, Malmerberg E, Martin AV, Messerschmidt M, Nass K, Redecke L, Seibert MM, Sjöhamn J, Steinbrener J, Stellato F, Wang D, Wahlgren WY, Weierstall U, Westenhoff S, Zatsepin NA, Boutet S, Spence JCH, Schlichting I, Chapman HN, Fromme P, Neutze R. Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography. Nat Commun 2014; 4:2911. [PMID: 24352554 PMCID: PMC3905732 DOI: 10.1038/ncomms3911] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 11/08/2013] [Indexed: 11/22/2022] Open
Abstract
Serial femtosecond crystallography is an X-ray free-electron-laser-based method with considerable potential to have an impact on challenging problems in structural biology. Here we present X-ray diffraction data recorded from microcrystals of the Blastochloris viridis photosynthetic reaction centre to 2.8 Å resolution and determine its serial femtosecond crystallography structure to 3.5 Å resolution. Although every microcrystal is exposed to a dose of 33 MGy, no signs of X-ray-induced radiation damage are visible in this integral membrane protein structure. Serial femtosecond crystallography is an X-ray free-electron-laser-based method that uses X-ray bursts to determine protein structures. Here the authors present the structure of a photosynthetic reaction centre, an integral membrane protein, achieved with no sign of X-ray-induced radiation damage.
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Lindner R, Lou X, Reinstein J, Shoeman RL, Hamprecht FA, Winkler A. Hexicon 2: automated processing of hydrogen-deuterium exchange mass spectrometry data with improved deuteration distribution estimation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1018-28. [PMID: 24676893 PMCID: PMC4018513 DOI: 10.1007/s13361-014-0850-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 02/05/2014] [Accepted: 02/05/2014] [Indexed: 05/12/2023]
Abstract
Hydrogen-deuterium exchange (HDX) experiments analyzed by mass spectrometry (MS) provide information about the dynamics and the solvent accessibility of protein backbone amide hydrogen atoms. Continuous improvement of MS instrumentation has contributed to the increasing popularity of this method; however, comprehensive automated data analysis is only beginning to mature. We present Hexicon 2, an automated pipeline for data analysis and visualization based on the previously published program Hexicon (Lou et al. 2010). Hexicon 2 employs the sensitive NITPICK peak detection algorithm of its predecessor in a divide-and-conquer strategy and adds new features, such as chromatogram alignment and improved peptide sequence assignment. The unique feature of deuteration distribution estimation was retained in Hexicon 2 and improved using an iterative deconvolution algorithm that is robust even to noisy data. In addition, Hexicon 2 provides a data browser that facilitates quality control and provides convenient access to common data visualization tasks. Analysis of a benchmark dataset demonstrates superior performance of Hexicon 2 compared with its predecessor in terms of deuteration centroid recovery and deuteration distribution estimation. Hexicon 2 greatly reduces data analysis time compared with manual analysis, whereas the increased number of peptides provides redundant coverage of the entire protein sequence. Hexicon 2 is a standalone application available free of charge under http://hx2.mpimf-heidelberg.mpg.de.
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Winkler A, Udvarhelyi A, Hartmann E, Reinstein J, Menzel A, Shoeman RL, Schlichting I. Characterization of elements involved in allosteric light regulation of phosphodiesterase activity by comparison of different functional BlrP1 states. J Mol Biol 2013; 426:853-68. [PMID: 24291457 PMCID: PMC3989770 DOI: 10.1016/j.jmb.2013.11.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 11/18/2013] [Accepted: 11/20/2013] [Indexed: 12/31/2022]
Abstract
Bacteria have evolved dedicated signaling mechanisms that enable the integration of a range of environmental stimuli and the accordant modulation of metabolic pathways. One central signaling molecule in bacteria is the second messenger cyclic dimeric GMP (c-di-GMP). Complex regulatory mechanisms for modulating c-di-GMP concentrations have evolved, in line with its importance for maintaining bacterial fitness under changing environmental conditions. One interesting example in this context is the blue-light-regulated phosphodiesterase 1 (BlrP1) of Klebsiella pneumoniae. This covalently linked system of a sensor of blue light using FAD (BLUF) and an EAL phosphodiesterase domain orchestrates the light-dependent down-regulation of c-di-GMP levels. To reveal details of light-induced structural changes involved in EAL activity regulation, we extended previous crystallographic studies with hydrogen–deuterium exchange experiments and small-angle X-ray scattering analysis of different functional BlrP1 states. The combination of hydrogen–deuterium exchange and small-angle X-ray scattering allows the integration of local and global structural changes and provides an improved understanding of light signaling via an allosteric communication pathway between the BLUF and EAL domains. This model is supported by results from a mutational analysis of the EAL dimerization region and the analysis of metal-coordination effects of the EAL active site on the dark-state recovery kinetics of the BLUF domain. In combination with structural information from other EAL domains, the observed bidirectional communication points to a general mechanism of EAL activity regulation and suggests that a similar allosteric coupling is maintained in catalytically inactive EAL domains that retain a regulatory function. C-di-GMP is a central bacterial signaling molecule integrating environmental stimuli. BlrP1 enables the light-regulated degradation of c-di-GMP. Light-induced structural changes involve subtle quaternary structure rearrangements. Light signal integration involves allosteric signaling between BLUF and EAL. Analysis of different functional states reveals details of this communication pathway.
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Park HJ, Loh ND, Sierra RG, Hampton CY, Starodub D, Martin AV, Barty A, Aquila A, Schulz J, Steinbrener J, Shoeman RL, Lomb L, Kassemeyer S, Bostedt C, Bozek J, Epp SW, Erk B, Hartmann R, Rolles D, Rudenko A, Rudek B, Foucar L, Kimmel N, Weidenspointner G, Hauser G, Holl P, Pedersoli E, Liang M, Hunter MS, Gumprecht L, Coppola N, Wunderer C, Graafsma H, Maia FRNC, Ekeberg T, Hantke M, Fleckenstein H, Hirsemann H, Nass K, Tobias HJ, Farquar GR, Benner WH, Hau-Riege S, Reich C, Hartmann A, Soltau H, Marchesini S, Bajt S, Barthelmess M, Strueder L, Ullrich J, Bucksbaum P, Frank M, Schlichting I, Chapman HN, Bogan MJ, Elser V. Toward unsupervised single-shot diffractive imaging of heterogeneous particles using X-ray free-electron lasers. OPTICS EXPRESS 2013; 21:28729-42. [PMID: 24514385 DOI: 10.1364/oe.21.028729] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Single shot diffraction imaging experiments via X-ray free-electron lasers can generate as many as hundreds of thousands of diffraction patterns of scattering objects. Recovering the real space contrast of a scattering object from these patterns currently requires a reconstruction process with user guidance in a number of steps, introducing severe bottlenecks in data processing. We present a series of measures that replace user guidance with algorithms that reconstruct contrasts in an unsupervised fashion. We demonstrate the feasibility of automating the reconstruction process by generating hundreds of contrasts obtained from soot particle diffraction experiments.
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Demirci H, Sierra RG, Laksmono H, Shoeman RL, Botha S, Barends TRM, Nass K, Schlichting I, Doak RB, Gati C, Williams GJ, Boutet S, Messerschmidt M, Jogl G, Dahlberg AE, Gregory ST, Bogan MJ. Serial femtosecond X-ray diffraction of 30S ribosomal subunit microcrystals in liquid suspension at ambient temperature using an X-ray free-electron laser. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1066-9. [PMID: 23989164 PMCID: PMC3758164 DOI: 10.1107/s174430911302099x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 07/27/2013] [Indexed: 12/03/2022]
Abstract
High-resolution ribosome structures determined by X-ray crystallography have provided important insights into the mechanism of translation. Such studies have thus far relied on large ribosome crystals kept at cryogenic temperatures to reduce radiation damage. Here, the application of serial femtosecond X-ray crystallography (SFX) using an X-ray free-electron laser (XFEL) to obtain diffraction data from ribosome microcrystals in liquid suspension at ambient temperature is described. 30S ribosomal subunit microcrystals diffracted to beyond 6 Å resolution, demonstrating the feasibility of using SFX for ribosome structural studies. The ability to collect diffraction data at near-physiological temperatures promises to provide fundamental insights into the structural dynamics of the ribosome and its functional complexes.
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Barends TRM, Brosi RWW, Steinmetz A, Scherer A, Hartmann E, Eschenbach J, Lorenz T, Seidel R, Shoeman RL, Zimmermann S, Bittl R, Schlichting I, Reinstein J. Combining crystallography and EPR: crystal and solution structures of the multidomain cochaperone DnaJ. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1540-52. [PMID: 23897477 PMCID: PMC3727329 DOI: 10.1107/s0907444913010640] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 04/18/2013] [Indexed: 11/15/2022]
Abstract
Hsp70 chaperones assist in a large variety of protein-folding processes in the cell. Crucial for these activities is the regulation of Hsp70 by Hsp40 cochaperones. DnaJ, the bacterial homologue of Hsp40, stimulates ATP hydrolysis by DnaK (Hsp70) and thus mediates capture of substrate protein, but is also known to possess chaperone activity of its own. The first structure of a complete functional dimeric DnaJ was determined and the mobility of its individual domains in solution was investigated. Crystal structures of the complete molecular cochaperone DnaJ from Thermus thermophilus comprising the J, GF and C-terminal domains and of the J and GF domains alone showed an ordered GF domain interacting with the J domain. Structure-based EPR spin-labelling studies as well as cross-linking results showed the existence of multiple states of DnaJ in solution with different arrangements of the various domains, which has implications for the function of DnaJ.
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Starodub D, Aquila A, Bajt S, Barthelmess M, Barty A, Bostedt C, Bozek JD, Coppola N, Doak RB, Epp SW, Erk B, Foucar L, Gumprecht L, Hampton CY, Hartmann A, Hartmann R, Holl P, Kassemeyer S, Kimmel N, Laksmono H, Liang M, Loh ND, Lomb L, Martin AV, Nass K, Reich C, Rolles D, Rudek B, Rudenko A, Schulz J, Shoeman RL, Sierra RG, Soltau H, Steinbrener J, Stellato F, Stern S, Weidenspointner G, Frank M, Ullrich J, Strüder L, Schlichting I, Chapman HN, Spence JCH, Bogan MJ. Single-particle structure determination by correlations of snapshot X-ray diffraction patterns. Nat Commun 2013; 3:1276. [PMID: 23232406 DOI: 10.1038/ncomms2288] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 11/14/2012] [Indexed: 11/09/2022] Open
Abstract
Diffractive imaging with free-electron lasers allows structure determination from ensembles of weakly scattering identical nanoparticles. The ultra-short, ultra-bright X-ray pulses provide snapshots of the randomly oriented particles frozen in time, and terminate before the onset of structural damage. As signal strength diminishes for small particles, the synthesis of a three-dimensional diffraction volume requires simultaneous involvement of all data. Here we report the first application of a three-dimensional spatial frequency correlation analysis to carry out this synthesis from noisy single-particle femtosecond X-ray diffraction patterns of nearly identical samples in random and unknown orientations, collected at the Linac Coherent Light Source. Our demonstration uses unsupported test particles created via aerosol self-assembly, and composed of two polystyrene spheres of equal diameter. The correlation analysis avoids the need for orientation determination entirely. This method may be applied to the structural determination of biological macromolecules in solution.
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Winkler A, Heintz U, Lindner R, Reinstein J, Shoeman RL, Schlichting I. A ternary AppA-PpsR-DNA complex mediates light regulation of photosynthesis-related gene expression. Nat Struct Mol Biol 2013; 20:859-67. [PMID: 23728293 PMCID: PMC3702404 DOI: 10.1038/nsmb.2597] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 04/10/2013] [Indexed: 11/09/2022]
Abstract
The anoxygenic phototrophic bacterium Rhodobacter sphaeroides uses different energy sources, depending on environmental conditions including aerobic respiration or, in the absence of oxygen, photosynthesis. Photosynthetic genes are repressed at high oxygen tension, but at intermediate levels their partial expression prepares the bacterium for using light energy. Illumination, however, enhances repression under semiaerobic conditions. Here, we describe molecular details of two proteins mediating oxygen and light control of photosynthesis-gene expression: the light-sensing antirepressor AppA and the transcriptional repressor PpsR. Our crystal structures of both proteins and their complex and hydrogen/deuterium-exchange data show that light activation of AppA-PpsR2 affects the PpsR effector region within the complex. DNA binding studies demonstrate the formation of a light-sensitive ternary AppA-PpsR-DNA complex. We discuss implications of these results for regulation by light and oxygen, highlighting new insights into blue light-mediated signal transduction.
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Loh ND, Starodub D, Lomb L, Hampton CY, Martin AV, Sierra RG, Barty A, Aquila A, Schulz J, Steinbrener J, Shoeman RL, Kassemeyer S, Bostedt C, Bozek J, Epp SW, Erk B, Hartmann R, Rolles D, Rudenko A, Rudek B, Foucar L, Kimmel N, Weidenspointner G, Hauser G, Holl P, Pedersoli E, Liang M, Hunter MS, Gumprecht L, Coppola N, Wunderer C, Graafsma H, Maia FRNC, Ekeberg T, Hantke M, Fleckenstein H, Hirsemann H, Nass K, White TA, Tobias HJ, Farquar GR, Benner WH, Hau-Riege S, Reich C, Hartmann A, Soltau H, Marchesini S, Bajt S, Barthelmess M, Strueder L, Ullrich J, Bucksbaum P, Frank M, Schlichting I, Chapman HN, Bogan MJ. Sensing the wavefront of x-ray free-electron lasers using aerosol spheres. OPTICS EXPRESS 2013; 21:12385-12394. [PMID: 23736456 DOI: 10.1364/oe.21.012385] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Characterizing intense, focused x-ray free electron laser (FEL) pulses is crucial for their use in diffractive imaging. We describe how the distribution of average phase tilts and intensities on hard x-ray pulses with peak intensities of 10(21) W/m(2) can be retrieved from an ensemble of diffraction patterns produced by 70 nm-radius polystyrene spheres, in a manner that mimics wavefront sensors. Besides showing that an adaptive geometric correction may be necessary for diffraction data from randomly injected sample sources, our paper demonstrates the possibility of collecting statistics on structured pulses using only the diffraction patterns they generate and highlights the imperative to study its impact on single-particle diffractive imaging.
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Barends TRM, Foucar L, Shoeman RL, Bari S, Epp SW, Hartmann R, Hauser G, Huth M, Kieser C, Lomb L, Motomura K, Nagaya K, Schmidt C, Strecker R, Anielski D, Boll R, Erk B, Fukuzawa H, Hartmann E, Hatsui T, Holl P, Inubushi Y, Ishikawa T, Kassemeyer S, Kaiser C, Koeck F, Kunishima N, Kurka M, Rolles D, Rudek B, Rudenko A, Sato T, Schroeter CD, Soltau H, Strueder L, Tanaka T, Togashi T, Tono K, Ullrich J, Yase S, Wada SI, Yao M, Yabashi M, Ueda K, Schlichting I. Anomalous signal from S atoms in protein crystallographic data from an X-ray free-electron laser. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:838-42. [PMID: 23633593 DOI: 10.1107/s0907444913002448] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 01/24/2013] [Indexed: 11/10/2022]
Abstract
X-ray free-electron lasers (FELs) enable crystallographic data collection using extremely bright femtosecond pulses from microscopic crystals beyond the limitations of conventional radiation damage. This diffraction-before-destruction approach requires a new crystal for each FEL shot and, since the crystals cannot be rotated during the X-ray pulse, data collection requires averaging over many different crystals and a Monte Carlo integration of the diffraction intensities, making the accurate determination of structure factors challenging. To investigate whether sufficient accuracy can be attained for the measurement of anomalous signal, a large data set was collected from lysozyme microcrystals at the newly established `multi-purpose spectroscopy/imaging instrument' of the SPring-8 Ångstrom Compact Free-Electron Laser (SACLA) at RIKEN Harima. Anomalous difference density maps calculated from these data demonstrate that serial femtosecond crystallography using a free-electron laser is sufficiently accurate to measure even the very weak anomalous signal of naturally occurring S atoms in a protein at a photon energy of 7.3 keV.
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Redecke L, Nass K, DePonte DP, White TA, Rehders D, Barty A, Stellato F, Liang M, Barends TR, Boutet S, Williams GJ, Messerschmidt M, Seibert MM, Aquila A, Arnlund D, Bajt S, Barth T, Bogan MJ, Caleman C, Chao TC, Doak RB, Fleckenstein H, Frank M, Fromme R, Galli L, Grotjohann I, Hunter MS, Johansson LC, Kassemeyer S, Katona G, Kirian RA, Koopmann R, Kupitz C, Lomb L, Martin AV, Mogk S, Neutze R, Shoeman RL, Steinbrener J, Timneanu N, Wang D, Weierstall U, Zatsepin NA, Spence JCH, Fromme P, Schlichting I, Duszenko M, Betzel C, Chapman HN. Natively inhibited Trypanosoma brucei cathepsin B structure determined by using an X-ray laser. Science 2013; 339:227-230. [PMID: 23196907 PMCID: PMC3786669 DOI: 10.1126/science.1229663] [Citation(s) in RCA: 356] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The Trypanosoma brucei cysteine protease cathepsin B (TbCatB), which is involved in host protein degradation, is a promising target to develop new treatments against sleeping sickness, a fatal disease caused by this protozoan parasite. The structure of the mature, active form of TbCatB has so far not provided sufficient information for the design of a safe and specific drug against T. brucei. By combining two recent innovations, in vivo crystallization and serial femtosecond crystallography, we obtained the room-temperature 2.1 angstrom resolution structure of the fully glycosylated precursor complex of TbCatB. The structure reveals the mechanism of native TbCatB inhibition and demonstrates that new biomolecular information can be obtained by the "diffraction-before-destruction" approach of x-ray free-electron lasers from hundreds of thousands of individual microcrystals.
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Boutet S, Lomb L, Williams GJ, Barends TRM, Aquila A, Doak RB, Weierstall U, DePonte DP, Steinbrener J, Shoeman RL, Messerschmidt M, Barty A, White TA, Kassemeyer S, Kirian RA, Seibert MM, Montanez PA, Kenney C, Herbst R, Hart P, Pines J, Haller G, Gruner SM, Philipp HT, Tate MW, Hromalik M, Koerner LJ, van Bakel N, Morse J, Ghonsalves W, Arnlund D, Bogan MJ, Caleman C, Fromme R, Hampton CY, Hunter MS, Johansson LC, Katona G, Kupitz C, Liang M, Martin AV, Nass K, Redecke L, Stellato F, Timneanu N, Wang D, Zatsepin NA, Schafer D, Defever J, Neutze R, Fromme P, Spence JCH, Chapman HN, Schlichting I. High-resolution protein structure determination by serial femtosecond crystallography. Science 2012; 337:362-4. [PMID: 22653729 PMCID: PMC3788707 DOI: 10.1126/science.1217737] [Citation(s) in RCA: 539] [Impact Index Per Article: 44.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules.
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Lomb L, Steinbrener J, Bari S, Beisel D, Berndt D, Kieser C, Lukat M, Neef N, Shoeman RL. An anti-settling sample delivery instrument for serial femtosecond crystallography. J Appl Crystallogr 2012. [DOI: 10.1107/s0021889812024557] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Serial femtosecond crystallography (SFX) using X-ray free-electron laser (FEL) sources has the potential to determine the structures of macromolecules beyond the limitation of radiation damage and without the need for crystals of sufficient size for conventional crystallography. In SFX, a liquid microjet is used to inject randomly oriented crystals suspended in their storage solution into the FEL beam. Settling of crystals in the reservoir prior to the injection has been found to complicate the data collection. This article details the development of an anti-settling sample delivery instrument based on a rotating syringe pump, capable of producing flow rates and liquid pressures necessary for the operation of the injector. The device has been used successfully with crystals of different proteins, with crystal sizes smaller than 20 µm. Even after hours of continuous operation, no significant impairment of the experiments due to sample settling was observed. This article describes the working principle of the instrument and sets it in context with regard to the experimental conditions used for SFX. Hit rates for longer measuring periods are compared with and without the instrument operating. Two versions of the instrument have been developed, which both deliver sample at a constant flow rate but which differ in their minimum liquid flow rates and maximum pressures.
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Loh ND, Hampton CY, Martin AV, Starodub D, Sierra RG, Barty A, Aquila A, Schulz J, Lomb L, Steinbrener J, Shoeman RL, Kassemeyer S, Bostedt C, Bozek J, Epp SW, Erk B, Hartmann R, Rolles D, Rudenko A, Rudek B, Foucar L, Kimmel N, Weidenspointner G, Hauser G, Holl P, Pedersoli E, Liang M, Hunter MS, Hunter MM, Gumprecht L, Coppola N, Wunderer C, Graafsma H, Maia FRNC, Ekeberg T, Hantke M, Fleckenstein H, Hirsemann H, Nass K, White TA, Tobias HJ, Farquar GR, Benner WH, Hau-Riege SP, Reich C, Hartmann A, Soltau H, Marchesini S, Bajt S, Barthelmess M, Bucksbaum P, Hodgson KO, Strüder L, Ullrich J, Frank M, Schlichting I, Chapman HN, Bogan MJ. Fractal morphology, imaging and mass spectrometry of single aerosol particles in flight. Nature 2012; 486:513-7. [PMID: 22739316 DOI: 10.1038/nature11222] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 05/09/2012] [Indexed: 11/09/2022]
Abstract
The morphology of micrometre-size particulate matter is of critical importance in fields ranging from toxicology to climate science, yet these properties are surprisingly difficult to measure in the particles' native environment. Electron microscopy requires collection of particles on a substrate; visible light scattering provides insufficient resolution; and X-ray synchrotron studies have been limited to ensembles of particles. Here we demonstrate an in situ method for imaging individual sub-micrometre particles to nanometre resolution in their native environment, using intense, coherent X-ray pulses from the Linac Coherent Light Source free-electron laser. We introduced individual aerosol particles into the pulsed X-ray beam, which is sufficiently intense that diffraction from individual particles can be measured for morphological analysis. At the same time, ion fragments ejected from the beam were analysed using mass spectrometry, to determine the composition of single aerosol particles. Our results show the extent of internal dilation symmetry of individual soot particles subject to non-equilibrium aggregation, and the surprisingly large variability in their fractal dimensions. More broadly, our methods can be extended to resolve both static and dynamic morphology of general ensembles of disordered particles. Such general morphology has implications in topics such as solvent accessibilities in proteins, vibrational energy transfer by the hydrodynamic interaction of amino acids, and large-scale production of nanoscale structures by flame synthesis.
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Martin AV, Loh ND, Hampton CY, Sierra RG, Wang F, Aquila A, Bajt S, Barthelmess M, Bostedt C, Bozek JD, Coppola N, Epp SW, Erk B, Fleckenstein H, Foucar L, Frank M, Graafsma H, Gumprecht L, Hartmann A, Hartmann R, Hauser G, Hirsemann H, Holl P, Kassemeyer S, Kimmel N, Liang M, Lomb L, Maia FRNC, Marchesini S, Nass K, Pedersoli E, Reich C, Rolles D, Rudek B, Rudenko A, Schulz J, Shoeman RL, Soltau H, Starodub D, Steinbrener J, Stellato F, Strüder L, Ullrich J, Weidenspointner G, White TA, Wunderer CB, Barty A, Schlichting I, Bogan MJ, Chapman HN. Femtosecond dark-field imaging with an X-ray free electron laser. OPTICS EXPRESS 2012; 20:13501-12. [PMID: 22714377 DOI: 10.1364/oe.20.013501] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The emergence of femtosecond diffractive imaging with X-ray lasers has enabled pioneering structural studies of isolated particles, such as viruses, at nanometer length scales. However, the issue of missing low frequency data significantly limits the potential of X-ray lasers to reveal sub-nanometer details of micrometer-sized samples. We have developed a new technique of dark-field coherent diffractive imaging to simultaneously overcome the missing data issue and enable us to harness the unique contrast mechanisms available in dark-field microscopy. Images of airborne particulate matter (soot) up to two microns in length were obtained using single-shot diffraction patterns obtained at the Linac Coherent Light Source, four times the size of objects previously imaged in similar experiments. This technique opens the door to femtosecond diffractive imaging of a wide range of micrometer-sized materials that exhibit irreproducible complexity down to the nanoscale, including airborne particulate matter, small cells, bacteria and gold-labeled biological samples.
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Kassemeyer S, Steinbrener J, Lomb L, Hartmann E, Aquila A, Barty A, Martin AV, Hampton CY, Bajt S, Barthelmess M, Barends TRM, Bostedt C, Bott M, Bozek JD, Coppola N, Cryle M, DePonte DP, Doak RB, Epp SW, Erk B, Fleckenstein H, Foucar L, Graafsma H, Gumprecht L, Hartmann A, Hartmann R, Hauser G, Hirsemann H, Hömke A, Holl P, Jönsson O, Kimmel N, Krasniqi F, Liang M, Maia FRNC, Marchesini S, Nass K, Reich C, Rolles D, Rudek B, Rudenko A, Schmidt C, Schulz J, Shoeman RL, Sierra RG, Soltau H, Spence JCH, Starodub D, Stellato F, Stern S, Stier G, Svenda M, Weidenspointner G, Weierstall U, White TA, Wunderer C, Frank M, Chapman HN, Ullrich J, Strüder L, Bogan MJ, Schlichting I. Femtosecond free-electron laser x-ray diffraction data sets for algorithm development. OPTICS EXPRESS 2012; 20:4149-58. [PMID: 22418172 DOI: 10.1364/oe.20.004149] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
We describe femtosecond X-ray diffraction data sets of viruses and nanoparticles collected at the Linac Coherent Light Source. The data establish the first large benchmark data sets for coherent diffraction methods freely available to the public, to bolster the development of algorithms that are essential for developing this novel approach as a useful imaging technique. Applications are 2D reconstructions, orientation classification and finally 3D imaging by assembling 2D patterns into a 3D diffraction volume.
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