Literature DB >> 21325716

Structure-factor analysis of femtosecond microdiffraction patterns from protein nanocrystals.

Richard A Kirian1, Thomas A White, James M Holton, Henry N Chapman, Petra Fromme, Anton Barty, Lukas Lomb, Andrew Aquila, Filipe R N C Maia, Andrew V Martin, Raimund Fromme, Xiaoyu Wang, Mark S Hunter, Kevin E Schmidt, John C H Spence.   

Abstract

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.

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Year:  2011        PMID: 21325716      PMCID: PMC3066792          DOI: 10.1107/S0108767310050981

Source DB:  PubMed          Journal:  Acta Crystallogr A        ISSN: 0108-7673            Impact factor:   2.290


  16 in total

1.  Three-dimensional structure of cyanobacterial photosystem I at 2.5 A resolution.

Authors:  P Jordan; P Fromme; H T Witt; O Klukas; W Saenger; N Krauss
Journal:  Nature       Date:  2001-06-21       Impact factor: 49.962

2.  Potential for biomolecular imaging with femtosecond X-ray pulses.

Authors:  R Neutze; R Wouts; D van der Spoel; E Weckert; J Hajdu
Journal:  Nature       Date:  2000-08-17       Impact factor: 49.962

3.  Refinement of macromolecular structures by the maximum-likelihood method.

Authors:  G N Murshudov; A A Vagin; E J Dodson
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1997-05-01

4.  X-ray diffraction from membrane protein nanocrystals.

Authors:  M S Hunter; D P DePonte; D A Shapiro; R A Kirian; X Wang; D Starodub; S Marchesini; U Weierstall; R B Doak; J C H Spence; P Fromme
Journal:  Biophys J       Date:  2011-01-05       Impact factor: 4.033

5.  Photosystem I at 4 A resolution represents the first structural model of a joint photosynthetic reaction centre and core antenna system.

Authors:  N Krauss; W D Schubert; O Klukas; P Fromme; H T Witt; W Saenger
Journal:  Nat Struct Biol       Date:  1996-11

6.  Femtosecond protein nanocrystallography-data analysis methods.

Authors:  Richard A Kirian; Xiaoyu Wang; Uwe Weierstall; Kevin E Schmidt; John C H Spence; Mark Hunter; Petra Fromme; Thomas White; Henry N Chapman; James Holton
Journal:  Opt Express       Date:  2010-03-15       Impact factor: 3.894

7.  An assessment of the resolution limitation due to radiation-damage in x-ray diffraction microscopy.

Authors:  M R Howells; T Beetz; H N Chapman; C Cui; J M Holton; C J Jacobsen; J Kirz; E Lima; S Marchesini; H Miao; D Sayre; D A Shapiro; J C H Spence; D Starodub
Journal:  J Electron Spectros Relat Phenomena       Date:  2009-03-01       Impact factor: 1.957

8.  A robust bulk-solvent correction and anisotropic scaling procedure.

Authors:  Pavel V Afonine; Ralf W Grosse-Kunstleve; Paul D Adams
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2005-06-24

9.  The minimum crystal size needed for a complete diffraction data set.

Authors:  James M Holton; Kenneth A Frankel
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-03-24

Review 10.  The integration of macromolecular diffraction data.

Authors:  Andrew G W Leslie
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2005-12-14
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  67 in total

1.  Room temperature femtosecond X-ray diffraction of photosystem II microcrystals.

Authors:  Jan Kern; Roberto Alonso-Mori; Julia Hellmich; Rosalie Tran; Johan Hattne; Hartawan Laksmono; Carina Glöckner; Nathaniel Echols; Raymond G Sierra; Jonas Sellberg; Benedikt Lassalle-Kaiser; Richard J Gildea; Pieter Glatzel; Ralf W Grosse-Kunstleve; Matthew J Latimer; Trevor A McQueen; Dörte DiFiore; Alan R Fry; Marc Messerschmidt; Alan Miahnahri; Donald W Schafer; M Marvin Seibert; Dimosthenis Sokaras; Tsu-Chien Weng; Petrus H Zwart; William E White; Paul D Adams; Michael J Bogan; Sébastien Boutet; Garth J Williams; Johannes Messinger; Nicholas K Sauter; Athina Zouni; Uwe Bergmann; Junko Yano; Vittal K Yachandra
Journal:  Proc Natl Acad Sci U S A       Date:  2012-06-04       Impact factor: 11.205

2.  Lipidic phase membrane protein serial femtosecond crystallography.

Authors:  Linda C Johansson; David Arnlund; Thomas A White; Gergely Katona; Daniel P Deponte; Uwe Weierstall; R Bruce Doak; Robert L Shoeman; Lukas Lomb; Erik Malmerberg; Jan Davidsson; Karol Nass; Mengning Liang; Jakob Andreasson; Andrew Aquila; Saša Bajt; Miriam Barthelmess; Anton Barty; Michael J Bogan; Christoph Bostedt; John D Bozek; Carl Caleman; Ryan Coffee; Nicola Coppola; Tomas Ekeberg; Sascha W Epp; Benjamin Erk; Holger Fleckenstein; Lutz Foucar; Heinz Graafsma; Lars Gumprecht; Janos Hajdu; Christina Y Hampton; Robert Hartmann; Andreas Hartmann; Günter Hauser; Helmut Hirsemann; Peter Holl; Mark S Hunter; Stephan Kassemeyer; Nils Kimmel; Richard A Kirian; Filipe R N C Maia; Stefano Marchesini; Andrew V Martin; Christian Reich; Daniel Rolles; Benedikt Rudek; Artem Rudenko; Ilme Schlichting; Joachim Schulz; M Marvin Seibert; Raymond G Sierra; Heike Soltau; Dmitri Starodub; Francesco Stellato; Stephan Stern; Lothar Strüder; Nicusor Timneanu; Joachim Ullrich; Weixiao Y Wahlgren; Xiaoyu Wang; Georg Weidenspointner; Cornelia Wunderer; Petra Fromme; Henry N Chapman; John C H Spence; Richard Neutze
Journal:  Nat Methods       Date:  2012-01-29       Impact factor: 28.547

Review 3.  Femtosecond nanocrystallography using X-ray lasers for membrane protein structure determination.

Authors:  Petra Fromme; John C H Spence
Journal:  Curr Opin Struct Biol       Date:  2011-08       Impact factor: 6.809

4.  De novo protein crystal structure determination from X-ray free-electron laser data.

Authors:  Thomas R M Barends; Lutz Foucar; Sabine Botha; R Bruce Doak; Robert L Shoeman; Karol Nass; Jason E Koglin; Garth J Williams; Sébastien Boutet; Marc Messerschmidt; Ilme Schlichting
Journal:  Nature       Date:  2013-11-24       Impact factor: 49.962

5.  Laue diffraction and time-resolved crystallography: a personal history.

Authors:  Keith Moffat
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2019-06-17       Impact factor: 4.226

Review 6.  Understanding pre-mRNA splicing through crystallography.

Authors:  Sara Espinosa; Lingdi Zhang; Xueni Li; Rui Zhao
Journal:  Methods       Date:  2017-05-12       Impact factor: 3.608

7.  Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers.

Authors:  Johan Hattne; Nathaniel Echols; Rosalie Tran; Jan Kern; Richard J Gildea; Aaron S Brewster; Roberto Alonso-Mori; Carina Glöckner; Julia Hellmich; Hartawan Laksmono; Raymond G Sierra; Benedikt Lassalle-Kaiser; Alyssa Lampe; Guangye Han; Sheraz Gul; Dörte DiFiore; Despina Milathianaki; Alan R Fry; Alan Miahnahri; William E White; Donald W Schafer; M Marvin Seibert; Jason E Koglin; Dimosthenis Sokaras; Tsu-Chien Weng; Jonas Sellberg; Matthew J Latimer; Pieter Glatzel; Petrus H Zwart; Ralf W Grosse-Kunstleve; Michael J Bogan; Marc Messerschmidt; Garth J Williams; Sébastien Boutet; Johannes Messinger; Athina Zouni; Junko Yano; Uwe Bergmann; Vittal K Yachandra; Paul D Adams; Nicholas K Sauter
Journal:  Nat Methods       Date:  2014-03-16       Impact factor: 28.547

8.  Direct phasing in femtosecond nanocrystallography. I. Diffraction characteristics.

Authors:  Joe P J Chen; John C H Spence; Rick P Millane
Journal:  Acta Crystallogr A Found Adv       Date:  2014-01-15       Impact factor: 2.290

Review 9.  Time-resolved crystallography and protein design: signalling photoreceptors and optogenetics.

Authors:  Keith Moffat
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2014-07-17       Impact factor: 6.237

Review 10.  Atomic resolution structure determination by the cryo-EM method MicroED.

Authors:  Shian Liu; Johan Hattne; Francis E Reyes; Silvia Sanchez-Martinez; M Jason de la Cruz; Dan Shi; Tamir Gonen
Journal:  Protein Sci       Date:  2016-08-19       Impact factor: 6.725

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