Crystallographic data processing for free-electron laser sources
Thomas A. White,Anton Barty,Francesco Stellato,James M. Holton,James M. Holton,Richard A. Kirian,Nadia A. Zatsepin,Henry N. Chapman +7 more
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TLDR
A processing pipeline for diffraction data acquired using the ‘serial crystallography’ methodology with a free-electron laser source is described with reference to the crystallographic analysis suite CrystFEL and the pre-processing program Cheetah.Abstract:
A processing pipeline for diffraction data acquired using the `serial crystallography' methodology with a free-electron laser source is described with reference to the crystallographic analysis suite CrystFEL and the pre-processing program Cheetah. A detailed analysis of the nature and impact of indexing ambiguities is presented. Simulations of the Monte Carlo integration scheme, which accounts for the partially recorded nature of the diffraction intensities, are presented and show that the integration of partial reflections could be made to converge more quickly if the bandwidth of the X-rays were to be increased by a small amount or if a slight convergence angle were introduced into the incident beam.read more
Citations
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Journal ArticleDOI
Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser
Yanyong Kang,X. Edward Zhou,Xiang Gao,Yuanzheng He,Wei Liu,Andrii Ishchenko,Anton Barty,Thomas A. White,Oleksandr Yefanov,Gye Won Han,Qingping Xu,Parker W. de Waal,Jiyuan Ke,M. H. Eileen Tan,Chenghai Zhang,Arne Moeller,Graham M. West,Bruce D. Pascal,Ned Van Eps,Lydia N. Caro,Sergey A. Vishnivetskiy,Regina J. Lee,Kelly Suino-Powell,Xin Gu,Kuntal Pal,Jinming Ma,Xiaoyong Zhi,Sébastien Boutet,Garth J. Williams,Marc Messerschmidt,Cornelius Gati,Nadia A. Zatsepin,Dingjie Wang,Daniel James,Shibom Basu,Shatabdi Roy-Chowdhury,Chelsie E. Conrad,Jesse Coe,Haiguang Liu,Stella Lisova,Christopher Kupitz,Ingo Grotjohann,Raimund Fromme,Yi Jiang,Minjia Tan,Huaiyu Yang,Jun Li,Meitian Wang,Zhong Zheng,Dianfan Li,Nicole Howe,Yingming Zhao,Jörg Standfuss,Kay Diederichs,Yuhui Dong,Clinton S. Potter,Bridget Carragher,Martin Caffrey,Hualiang Jiang,Henry N. Chapman,John C. H. Spence,Petra Fromme,Uwe Weierstall,Oliver P. Ernst,Vsevolod Katritch,Vsevolod V. Gurevich,Patrick R. Griffin,Wayne L. Hubbell,Raymond C. Stevens,Vadim Cherezov,Karsten Melcher,H. Eric Xu +71 more
TL;DR: The crystal structure of a constitutively active form of human rhodopsin bound to a pre-activated form of the mouse visual arrestin is determined by serial femtosecond X-ray laser crystallography and provides a basis for understanding GPCR-mediated arrestin-biased signalling.
Journal ArticleDOI
Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography
Uwe Weierstall,Daniel James,Chong Wang,Thomas A. White,Dingjie Wang,Wei Liu,John C. H. Spence,R. Bruce Doak,Garrett Nelson,Petra Fromme,Raimund Fromme,Ingo Grotjohann,Christopher Kupitz,Nadia A. Zatsepin,Haiguang Liu,Shibom Basu,Daniel Wacker,Gye Won Han,Vsevolod Katritch,Sébastien Boutet,Marc Messerschmidt,Garth J. Williams,Jason E. Koglin,M. Marvin Seibert,M. Marvin Seibert,Markus Klinker,Cornelius Gati,Robert L. Shoeman,Anton Barty,Henry N. Chapman,Richard A. Kirian,Kenneth R. Beyerlein,Raymond C. Stevens,Dianfan Li,Syed T. A. Shah,Nicole Howe,Martin Caffrey,Vadim Cherezov +37 more
TL;DR: This work presents a technique for extruding gel-like LCP with embedded membrane protein microcrystals, providing a continuously renewed source of material for serial femtosecond crystallography.
Journal ArticleDOI
Serial femtosecond crystallography of G protein-coupled receptors.
Wei Liu,Daniel Wacker,Cornelius Gati,Gye Won Han,Daniel James,Dingjie Wang,Garrett Nelson,Uwe Weierstall,Vsevolod Katritch,Anton Barty,Nadia A. Zatsepin,Dianfan Li,Marc Messerschmidt,Sébastien Boutet,Garth J. Williams,Jason E. Koglin,M. Marvin Seibert,M. Marvin Seibert,Chong Wang,Syed T. A. Shah,Shibom Basu,Raimund Fromme,Christopher Kupitz,Kimberly N. Rendek,Ingo Grotjohann,Petra Fromme,Richard A. Kirian,Kenneth R. Beyerlein,Thomas A. White,Henry N. Chapman,Martin Caffrey,John C. H. Spence,Raymond C. Stevens,Vadim Cherezov +33 more
TL;DR: The structure of a human serotonin receptor was solved using a free-electron laser to analyze microcrystals and displays a distinct distribution of thermal motions and conformations of residues that likely more accurately represent the receptor structure and dynamics in a cellular environment.
Journal ArticleDOI
Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation.
Thomas R. M. Barends,Lutz Foucar,Albert Ardevol,Karol Nass,Andrew Aquila,Sabine Botha,R. Bruce Doak,Konstantin Falahati,Elisabeth Hartmann,M. Hilpert,Marcel Heinz,Marcel Heinz,Matthias C. Hoffmann,Jürgen Köfinger,Jason E. Koglin,Gabriela Kovacsova,Mengning Liang,Despina Milathianaki,Henrik T. Lemke,Jochen Reinstein,C.M. Roome,Robert L. Shoeman,Garth J. Williams,Irene Burghardt,Gerhard Hummer,Sébastien Boutet,Ilme Schlichting +26 more
TL;DR: Time-resolved serial femtosecond crystallography at an x-ray free-electron laser is used to resolve the ultrafast structural changes in the carbonmonoxy myoglobin complex upon photolysis of the Fe-CO bond and supports the prediction that an immediate collective response of the protein occurs upon ligand dissociation.
References
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Book ChapterDOI
Processing of X-ray diffraction data collected in oscillation mode
Zbyszek Otwinowski,Wladek Minor +1 more
TL;DR: The methods presented in the chapter have been applied to solve a large variety of problems, from inorganic molecules with 5 A unit cell to rotavirus of 700 A diameters crystallized in 700 × 1000 × 1400 A cell.
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First lasing and operation of an ångstrom-wavelength free-electron laser
Paul Emma,R. Akre,J. Arthur,Richard M. Bionta,Christoph Bostedt,John D. Bozek,Axel Brachmann,Philip H. Bucksbaum,Ryan Coffee,F.-J. Decker,Y. Ding,David H. Dowell,S. A. Edstrom,Alan Fisher,Josef Frisch,Sasha Gilevich,Jerome B. Hastings,G. Hays,Ph. Hering,Zhirong Huang,R. H. Iverson,Henrik Loos,Marc Messerschmidt,A. Miahnahri,Stefan Moeller,Heinz-Dieter Nuhn,G. Pile,Daniel Ratner,J. Rzepiela,D. Schultz,T. Smith,P. Stefan,H. Tompkins,Joshua J. Turner,J. Welch,William E. White,Juhao Wu,Gerald Yocky,J. Galayda +38 more
TL;DR: The Linac Coherent Light Source free-electron laser has achieved coherent X-ray generation down to a wavelength of 1.2 A and at a brightness that is nearly ten orders of magnitude higher than conventional synchrotrons.
Journal ArticleDOI
Potential for biomolecular imaging with femtosecond X-ray pulses
TL;DR: Computer simulations are used to investigate the structural information that can be recovered from the scattering of intense femtosecond X-ray pulses by single protein molecules and small assemblies and predict that ultrashort, high-intensity X-rays from free-electron lasers that are currently under development will provide a new approach to structural determinations with X- rays.
Journal ArticleDOI
Femtosecond X-ray protein nanocrystallography
Henry N. Chapman,Petra Fromme,Anton Barty,Thomas A. White,Richard A. Kirian,Andrew Aquila,Mark S. Hunter,Joachim Schulz,Daniel P. DePonte,Uwe Weierstall,R. Bruce Doak,Filipe R. N. C. Maia,Andrew V. Martin,Ilme Schlichting,Lukas Lomb,Nicola Coppola,Robert L. Shoeman,Sascha W. Epp,Robert Hartmann,Daniel Rolles,Artem Rudenko,Lutz Foucar,Nils Kimmel,Georg Weidenspointner,Peter Holl,Mengning Liang,Miriam Barthelmess,Carl Caleman,Sébastien Boutet,Michael J. Bogan,Jacek Krzywinski,Christoph Bostedt,Saša Bajt,Lars Gumprecht,Benedikt Rudek,Benjamin Erk,Carlo Schmidt,André Hömke,Christian Reich,Daniel Pietschner,Lothar Strüder,Günter Hauser,H. Gorke,Joachim Ullrich,Sven Herrmann,Gerhard Schaller,Florian Schopper,Heike Soltau,Kai-Uwe Kühnel,Marc Messerschmidt,John D. Bozek,Stefan P. Hau-Riege,Matthias Frank,Christina Y. Hampton,Raymond G. Sierra,Dmitri Starodub,Garth J. Williams,Janos Hajdu,Nicusor Timneanu,M. Marvin Seibert,M. Marvin Seibert,Jakob Andreasson,Andrea Rocker,Olof Jönsson,Martin Svenda,Stephan Stern,Karol Nass,Robert Andritschke,Claus Dieter Schröter,Faton Krasniqi,Mario Bott,Kevin Schmidt,Xiaoyu Wang,Ingo Grotjohann,James M. Holton,Thomas R. M. Barends,Richard Neutze,Stefano Marchesini,Raimund Fromme,Sebastian Schorb,Daniela Rupp,M. Adolph,Tais Gorkhover,Inger Andersson,Helmut Hirsemann,Guillaume Potdevin,Heinz Graafsma,Björn Nilsson,John C. H. Spence +88 more
TL;DR: This work 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, by using pulses briefer than the timescale of most damage processes.
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Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography
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