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1.  Single mimivirus particles intercepted and imaged with an X-ray laser 
Seibert, M. Marvin | Ekeberg, Tomas | Maia, Filipe R. N. C. | Svenda, Martin | Andreasson, Jakob | Jönsson, Olof | Odić, Duško | Iwan, Bianca | Rocker, Andrea | Westphal, Daniel | Hantke, Max | DePonte, Daniel P. | Barty, Anton | Schulz, Joachim | Gumprecht, Lars | Coppola, Nicola | Aquila, Andrew | Liang, Mengning | White, Thomas A. | Martin, Andrew | Caleman, Carl | Stern, Stephan | Abergel, Chantal | Seltzer, Virginie | Claverie, Jean-Michel | Bostedt, Christoph | Bozek, John D. | Boutet, Sébastien | Miahnahri, A. Alan | Messerschmidt, Marc | Krzywinski, Jacek | Williams, Garth | Hodgson, Keith O. | Bogan, Michael J. | Hampton, Christina Y. | Sierra, Raymond G. | Starodub, Dmitri | Andersson, Inger | Bajt, Saša | Barthelmess, Miriam | Spence, John C. H. | Fromme, Petra | Weierstall, Uwe | Kirian, Richard | Hunter, Mark | Doak, R. Bruce | Marchesini, Stefano | Hau-Riege, Stefan P. | Frank, Matthias | Shoeman, Robert L. | Lomb, Lukas | Epp, Sascha W. | Hartmann, Robert | Rolles, Daniel | Rudenko, Artem | Schmidt, Carlo | Foucar, Lutz | Kimmel, Nils | Holl, Peter | Rudek, Benedikt | Erk, Benjamin | Hömke, André | Reich, Christian | Pietschner, Daniel | Weidenspointner, Georg | Strüder, Lothar | Hauser, Günter | Gorke, Hubert | Ullrich, Joachim | Schlichting, Ilme | Herrmann, Sven | Schaller, Gerhard | Schopper, Florian | Soltau, Heike | Kühnel, Kai-Uwe | Andritschke, Robert | Schröter, Claus-Dieter | Krasniqi, Faton | Bott, Mario | Schorb, Sebastian | Rupp, Daniela | Adolph, Marcus | Gorkhover, Tais | Hirsemann, Helmut | Potdevin, Guillaume | Graafsma, Heinz | Nilsson, Björn | Chapman, Henry N. | Hajdu, Janos
Nature  2011;470(7332):78-81.
X-ray lasers offer new capabilities in understanding the structure of biological systems, complex materials and matter under extreme conditions1–4. Very short and extremely bright, coherent X-ray pulses can be used to outrun key damage processes and obtain a single diffraction pattern from a large macromolecule, a virus or a cell before the sample explodes and turns into plasma1. The continuous diffraction pattern of non-crystalline objects permits oversampling and direct phase retrieval2. Here we show that high-quality diffraction data can be obtained with a single X-ray pulse from a non-crystalline biological sample, a single mimivirus particle, which was injected into the pulsed beam of a hard-X-ray free-electron laser, the Linac Coherent Light Source5. Calculations indicate that the energy deposited into the virus by the pulse heated the particle to over 100,000 K after the pulse had left the sample. The reconstructed exit wavefront (image) yielded 32-nm full-period resolution in a single exposure and showed no measurable damage. The reconstruction indicates inhomogeneous arrangement of dense material inside the virion. We expect that significantly higher resolutions will be achieved in such experiments with shorter and brighter photon pulses focused to a smaller area. The resolution in such experiments can be further extended for samples available in multiple identical copies.
doi:10.1038/nature09748
PMCID: PMC4038304  PMID: 21293374
2.  Cheetah: software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data 
Journal of Applied Crystallography  2014;47(Pt 3):1118-1131.
The emerging technique of serial X-ray diffraction requires new software tools for the efficient analysis of large volumes of data. Event selection early in the analysis pipeline is highly advantageous. The described software for classifying, sorting and analysing events is freely available to the general community.
The emerging technique of serial X-ray diffraction, in which diffraction data are collected from samples flowing across a pulsed X-ray source at repetition rates of 100 Hz or higher, has necessitated the development of new software in order to handle the large data volumes produced. Sorting of data according to different criteria and rapid filtering of events to retain only diffraction patterns of interest results in significant reductions in data volume, thereby simplifying subsequent data analysis and management tasks. Meanwhile the generation of reduced data in the form of virtual powder patterns, radial stacks, histograms and other meta data creates data set summaries for analysis and overall experiment evaluation. Rapid data reduction early in the analysis pipeline is proving to be an essential first step in serial imaging experiments, prompting the authors to make the tool described in this article available to the general community. Originally developed for experiments at X-ray free-electron lasers, the software is based on a modular facility-independent library to promote portability between different experiments and is available under version 3 or later of the GNU General Public License.
doi:10.1107/S1600576714007626
PMCID: PMC4038800  PMID: 24904246
free-electron lasers; serial crystallography; serial X-ray diffraction
3.  Radiation damage in protein serial femtosecond crystallography using an x-ray free-electron laser 
X-ray free-electron lasers deliver intense femtosecond pulses that promise to yield high resolution diffraction data of nanocrystals before the destruction of the sample by radiation damage. Diffraction intensities of lysozyme nanocrystals collected at the Linac Coherent Light Source using 2 keV photons were used for structure determination by molecular replacement and analyzed for radiation damage as a function of pulse length and fluence. Signatures of radiation damage are observed for pulses as short as 70 fs. Parametric scaling used in conventional crystallography does not account for the observed effects.
doi:10.1103/PhysRevB.84.214111
PMCID: PMC3786679  PMID: 24089594
4.  Self-terminating diffraction gates femtosecond X-ray nanocrystallography measurements 
Nature photonics  2011;6:35-40.
X-ray free-electron lasers have enabled new approaches to the structural determination of protein crystals that are too small or radiation-sensitive for conventional analysis1. For sufficiently short pulses, diffraction is collected before significant changes occur to the sample, and it has been predicted that pulses as short as 10 fs may be required to acquire atomic-resolution structural information1–4. Here, we describe a mechanism unique to ultrafast, ultra-intense X-ray experiments that allows structural information to be collected from crystalline samples using high radiation doses without the requirement for the pulse to terminate before the onset of sample damage. Instead, the diffracted X-rays are gated by a rapid loss of crystalline periodicity, producing apparent pulse lengths significantly shorter than the duration of the incident pulse. The shortest apparent pulse lengths occur at the highest resolution, and our measurements indicate that current X-ray free-electron laser technology5 should enable structural determination from submicrometre protein crystals with atomic resolution.
doi:10.1038/nphoton.2011.297
PMCID: PMC3783007  PMID: 24078834
5.  Time-resolved protein nanocrystallography using an X-ray free-electron laser 
Aquila, Andrew | Hunter, Mark S. | Doak, R. Bruce | Kirian, Richard A. | Fromme, Petra | White, Thomas A. | Andreasson, Jakob | Arnlund, David | Bajt, Saša | Barends, Thomas R. M. | Barthelmess, Miriam | Bogan, Michael J. | Bostedt, Christoph | Bottin, Hervé | Bozek, John D. | Caleman, Carl | Coppola, Nicola | Davidsson, Jan | DePonte, Daniel P. | Elser, Veit | Epp, Sascha W. | Erk, Benjamin | Fleckenstein, Holger | Foucar, Lutz | Frank, Matthias | Fromme, Raimund | Graafsma, Heinz | Grotjohann, Ingo | Gumprecht, Lars | Hajdu, Janos | Hampton, Christina Y. | Hartmann, Andreas | Hartmann, Robert | Hau-Riege, Stefan | Hauser, Günter | Hirsemann, Helmut | Holl, Peter | Holton, James M. | Hömke, André | Johansson, Linda | Kimmel, Nils | Kassemeyer, Stephan | Krasniqi, Faton | Kühnel, Kai-Uwe | Liang, Mengning | Lomb, Lukas | Malmerberg, Erik | Marchesini, Stefano | Martin, Andrew V. | Maia, Filipe R.N.C. | Messerschmidt, Marc | Nass, Karol | Reich, Christian | Neutze, Richard | Rolles, Daniel | Rudek, Benedikt | Rudenko, Artem | Schlichting, Ilme | Schmidt, Carlo | Schmidt, Kevin E. | Schulz, Joachim | Seibert, M. Marvin | Shoeman, Robert L. | Sierra, Raymond | Soltau, Heike | Starodub, Dmitri | Stellato, Francesco | Stern, Stephan | Strüder, Lothar | Timneanu, Nicusor | Ullrich, Joachim | Wang, Xiaoyu | Williams, Garth J. | Weidenspointner, Georg | Weierstall, Uwe | Wunderer, Cornelia | Barty, Anton | Spence, John C. H. | Chapman, Henry N.
Optics Express  2012;20(3):2706-2716.
We demonstrate the use of an X-ray free electron laser synchronized with an optical pump laser to obtain X-ray diffraction snapshots from the photoactivated states of large membrane protein complexes in the form of nanocrystals flowing in a liquid jet. Light-induced changes of Photosystem I-Ferredoxin co-crystals were observed at time delays of 5 to 10 µs after excitation. The result correlates with the microsecond kinetics of electron transfer from Photosystem I to ferredoxin. The undocking process that follows the electron transfer leads to large rearrangements in the crystals that will terminally lead to the disintegration of the crystals. We describe the experimental setup and obtain the first time-resolved femtosecond serial X-ray crystallography results from an irreversible photo-chemical reaction at the Linac Coherent Light Source. This technique opens the door to time-resolved structural studies of reaction dynamics in biological systems.
doi:10.1364/OE.20.002706
PMCID: PMC3413412  PMID: 22330507
(170.7160) Ultrafast technology; (170.7440) X-ray imaging; (140.3450) Laser-induced chemistry; (140.7090) Ultrafast lasers; (170.0170) Medical optics and biotechnology
6.  Lipidic phase membrane protein serial femtosecond crystallography 
Nature methods  2012;9(3):263-265.
X-ray free electron laser (X-feL)-based serial femtosecond crystallography is an emerging method with potential to rapidly advance the challenging field of membrane protein structural biology. here we recorded interpretable diffraction data from micrometer-sized lipidic sponge phase crystals of the Blastochloris viridis photosynthetic reaction center delivered into an X-feL beam using a sponge phase micro-jet.
doi:10.1038/nmeth.1867
PMCID: PMC3438231  PMID: 22286383
7.  Femtosecond X-ray protein nanocrystallography 
Chapman, Henry N. | Fromme, Petra | Barty, Anton | White, Thomas A. | Kirian, Richard A. | Aquila, Andrew | Hunter, Mark S. | Schulz, Joachim | DePonte, Daniel P. | Weierstall, Uwe | Doak, R. Bruce | Maia, Filipe R. N. C. | Martin, Andrew V. | Schlichting, Ilme | Lomb, Lukas | Coppola, Nicola | Shoeman, Robert L. | Epp, Sascha W. | Hartmann, Robert | Rolles, Daniel | Rudenko, Artem | Foucar, Lutz | Kimmel, Nils | Weidenspointner, Georg | Holl, Peter | Liang, Mengning | Barthelmess, Miriam | Caleman, Carl | Boutet, Sébastien | Bogan, Michael J. | Krzywinski, Jacek | Bostedt, Christoph | Bajt, Saša | Gumprecht, Lars | Rudek, Benedikt | Erk, Benjamin | Schmidt, Carlo | Hömke, André | Reich, Christian | Pietschner, Daniel | Strüder, Lothar | Hauser, Günter | Gorke, Hubert | Ullrich, Joachim | Herrmann, Sven | Schaller, Gerhard | Schopper, Florian | Soltau, Heike | Kühnel, Kai-Uwe | Messerschmidt, Marc | Bozek, John D. | Hau-Riege, Stefan P. | Frank, Matthias | Hampton, Christina Y. | Sierra, Raymond G. | Starodub, Dmitri | Williams, Garth J. | Hajdu, Janos | Timneanu, Nicusor | Seibert, M. Marvin | Andreasson, Jakob | Rocker, Andrea | Jönsson, Olof | Svenda, Martin | Stern, Stephan | Nass, Karol | Andritschke, Robert | Schröter, Claus-Dieter | Krasniqi, Faton | Bott, Mario | Schmidt, Kevin E. | Wang, Xiaoyu | Grotjohann, Ingo | Holton, James M. | Barends, Thomas R. M. | Neutze, Richard | Marchesini, Stefano | Fromme, Raimund | Schorb, Sebastian | Rupp, Daniela | Adolph, Marcus | Gorkhover, Tais | Andersson, Inger | Hirsemann, Helmut | Potdevin, Guillaume | Graafsma, Heinz | Nilsson, Björn | Spence, John C. H.
Nature  2011;470(7332):73-77.
X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded1-3. It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction ‘snapshots’ are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source4. We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes5. More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (~200 nm to 2 μm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes6. This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage.
doi:10.1038/nature09750
PMCID: PMC3429598  PMID: 21293373
8.  In vivo protein crystallization opens new routes in structural biology 
Nature methods  2012;9(3):259-262.
Protein crystallization in cells has been observed several times in nature. However, owing to their small size these crystals have not yet been used for X-ray crystallographic analysis. We prepared nano-sized in vivo–grown crystals of Trypanosoma brucei enzymes and applied the emerging method of free-electron laser-based serial femtosecond crystallography to record interpretable diffraction data. This combined approach will open new opportunities in structural systems biology.
doi:10.1038/nmeth.1859
PMCID: PMC3429599  PMID: 22286384
9.  Time-resolved protein nanocrystallography using an X-ray free-electron laser 
Aquila, Andrew | Hunter, Mark S | Bruce Doak, R. | Kirian, Richard A. | Fromme, Petra | White, Thomas A. | Andreasson, Jakob | Arnlund, David | Bajt, Saša | Barends, Thomas R. M. | Barthelmess, Miriam | Bogan, Michael J. | Bostedt, Christoph | Bottin, Hervé | Bozek, John D. | Caleman, Carl | Coppola, Nicola | Davidsson, Jan | DePonte, Daniel P. | Elser, Veit | Epp, Sascha W. | Erk, Benjamin | Fleckenstein, Holger | Foucar, Lutz | Frank, Matthias | Fromme, Raimund | Graafsma, Heinz | Grotjohann, Ingo | Gumprecht, Lars | Hajdu, Janos | Hampton, Christina Y. | Hartmann, Andreas | Hartmann, Robert | Hau-Riege, Stefan | Hauser, Günter | Hirsemann, Helmut | Holl, Peter | Holton, James M. | Hömke, André | Johansson, Linda | Kimmel, Nils | Kassemeyer, Stephan | Krasniqi, Faton | Kühnel, Kai-Uwe | Liang, Mengning | Lomb, Lukas | Malmerberg, Erik | Marchesini, Stefano | Martin, Andrew V. | Maia, Filipe R.N.C. | Messerschmidt, Marc | Nass, Karol | Reich, Christian | Neutze, Richard | Rolles, Daniel | Rudek, Benedikt | Rudenko, Artem | Schlichting, Ilme | Schmidt, Carlo | Schmidt, Kevin E. | Schulz, Joachim | Seibert, M. Marvin | Shoeman, Robert L. | Sierra, Raymond | Soltau, Heike | Starodub, Dmitri | Stellato, Francesco | Stern, Stephan | Strüder, Lothar | Timneanu, Nicusor | Ullrich, Joachim | Wang, Xiaoyu | Williams, Garth J. | Weidenspointner, Georg | Weierstall, Uwe | Wunderer, Cornelia | Barty, Anton | Spence, John C. H | Chapman, Henry N.
Optics express  2012;20(3):2706-2716.
We demonstrate the use of an X-ray free electron laser synchronized with an optical pump laser to obtain X-ray diffraction snapshots from the photoactivated states of large membrane protein complexes in the form of nanocrystals flowing in a liquid jet. Light-induced changes of Photosystem I-Ferredoxin co-crystals were observed at time delays of 5 to 10 μs after excitation. The result correlates with the microsecond kinetics of electron transfer from Photosystem I to ferredoxin. The undocking process that follows the electron transfer leads to large rearrangements in the crystals that will terminally lead to the disintegration of the crystals. We describe the experimental setup and obtain the first time-resolved femtosecond serial X-ray crystallography results from an irreversible photo-chemical reaction at the Linac Coherent Light Source. This technique opens the door to time-resolved structural studies of reaction dynamics in biological systems.
PMCID: PMC3413412  PMID: 22330507
10.  Structure-factor analysis of femtosecond microdiffraction patterns from protein nanocrystals 
A complete set of structure factors has been extracted from hundreds of thousands of femtosecond X-ray diffraction patterns from randomly oriented Photosystem I membrane protein nanocrystals, using the Monte Carlo method of intensity integration. The data, collected at the Linac Coherent Light Source, are compared with conventional single-crystal data collected at a synchrotron source, and the quality of each data set was found to be similar.
A complete set of structure factors has been extracted from hundreds of thousands of femtosecond single-shot X-ray microdiffraction patterns taken from randomly oriented nanocrystals. The method of Monte Carlo integration over crystallite size and orientation was applied to experimental data from Photosystem I nanocrystals. This arrives at structure factors from many partial reflections without prior knowledge of the particle-size distribution. The data were collected at the Linac Coherent Light Source (the first hard-X-ray laser user facility), to which was fitted a hydrated protein nanocrystal injector jet, according to the method of serial crystallography. The data are single ‘still’ diffraction snapshots, each from a different nanocrystal with sizes ranging between 100 nm and 2 µm, so the angular width of Bragg peaks was dominated by crystal-size effects. These results were compared with single-crystal data recorded from large crystals of Photosystem I at the Advanced Light Source and the quality of the data was found to be similar. The implications for improving the efficiency of data collection by allowing the use of very small crystals, for radiation-damage reduction and for time-resolved diffraction studies at room temperature are discussed.
doi:10.1107/S0108767310050981
PMCID: PMC3066792  PMID: 21325716
nanocrystals; femtosecond diffraction; free-electron lasers; Monte Carlo methods; protein microdiffraction

Results 1-10 (10)