Literature DB >> 24633409

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

Johan Hattne1, Nathaniel Echols1, Rosalie Tran1, Jan Kern1, Richard J Gildea2, Aaron S Brewster1, Roberto Alonso-Mori3, Carina Glöckner4, Julia Hellmich4, Hartawan Laksmono5, Raymond G Sierra5, Benedikt Lassalle-Kaiser1, Alyssa Lampe1, Guangye Han1, Sheraz Gul1, Dörte DiFiore4, Despina Milathianaki3, Alan R Fry3, Alan Miahnahri3, William E White3, Donald W Schafer3, M Marvin Seibert3, Jason E Koglin3, Dimosthenis Sokaras6, Tsu-Chien Weng6, Jonas Sellberg7, Matthew J Latimer6, Pieter Glatzel8, Petrus H Zwart1, Ralf W Grosse-Kunstleve1, Michael J Bogan9, Marc Messerschmidt3, Garth J Williams3, Sébastien Boutet3, Johannes Messinger10, Athina Zouni11, Junko Yano1, Uwe Bergmann3, Vittal K Yachandra1, Paul D Adams1, Nicholas K Sauter1.   

Abstract

X-ray free-electron laser (XFEL) sources enable the use of crystallography to solve three-dimensional macromolecular structures under native conditions and without radiation damage. Results to date, however, have been limited by the challenge of deriving accurate Bragg intensities from a heterogeneous population of microcrystals, while at the same time modeling the X-ray spectrum and detector geometry. Here we present a computational approach designed to extract meaningful high-resolution signals from fewer diffraction measurements.

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Year:  2014        PMID: 24633409      PMCID: PMC4008696          DOI: 10.1038/nmeth.2887

Source DB:  PubMed          Journal:  Nat Methods        ISSN: 1548-7091            Impact factor:   28.547


  41 in total

1.  Data processing.

Authors:  M G Rossmann; C G van Beek
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1999-10

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.  Amino-acid sequence of thermolysin.

Authors:  K Titani; M A Hermodson; L H Ericsson; K A Walsh; H Neurath
Journal:  Nat New Biol       Date:  1972-07-12

4.  Nanoflow electrospinning serial femtosecond crystallography.

Authors:  Raymond G Sierra; Hartawan Laksmono; Jan Kern; Rosalie Tran; Johan Hattne; Roberto Alonso-Mori; Benedikt Lassalle-Kaiser; Carina Glöckner; Julia Hellmich; Donald W Schafer; Nathaniel Echols; Richard J Gildea; Ralf W Grosse-Kunstleve; Jonas Sellberg; Trevor A McQueen; Alan R Fry; Marc M Messerschmidt; Alan Miahnahri; M Marvin Seibert; Christina Y Hampton; Dmitri Starodub; N Duane Loh; Dimosthenis Sokaras; Tsu-Chien Weng; Petrus H Zwart; Pieter Glatzel; Despina Milathianaki; William E White; Paul D Adams; Garth J Williams; Sébastien Boutet; Athina Zouni; Johannes Messinger; Nicholas K Sauter; Uwe Bergmann; Junko Yano; Vittal K Yachandra; Michael J Bogan
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2012-10-18

Review 5.  X-ray free electron lasers motivate bioanalytical characterization of protein nanocrystals: serial femtosecond crystallography.

Authors:  Michael J Bogan
Journal:  Anal Chem       Date:  2013-03-21       Impact factor: 6.986

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.  Autoindexing with outlier rejection and identification of superimposed lattices.

Authors:  Nicholas K Sauter; Billy K Poon
Journal:  J Appl Crystallogr       Date:  2010-04-30       Impact factor: 3.304

8.  New Python-based methods for data processing.

Authors:  Nicholas K Sauter; Johan Hattne; Ralf W Grosse-Kunstleve; Nathaniel Echols
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2013-06-18

9.  Better models by discarding data?

Authors:  K Diederichs; P A Karplus
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2013-06-15

10.  Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard.

Authors:  Thomas C Terwilliger; Ralf W Grosse-Kunstleve; Pavel V Afonine; Nigel W Moriarty; Peter H Zwart; Li Wei Hung; Randy J Read; Paul D Adams
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2007-12-05
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  88 in total

1.  Accurate determination of segmented X-ray detector geometry.

Authors:  Oleksandr Yefanov; Valerio Mariani; Cornelius Gati; Thomas A White; Henry N Chapman; Anton Barty
Journal:  Opt Express       Date:  2015-11-02       Impact factor: 3.894

2.  Progress in protein crystallography.

Authors:  Zbigniew Dauter; Alexander Wlodawer
Journal:  Protein Pept Lett       Date:  2016       Impact factor: 1.890

Review 3.  A Bright Future for Serial Femtosecond Crystallography with XFELs.

Authors:  Linda C Johansson; Benjamin Stauch; Andrii Ishchenko; Vadim Cherezov
Journal:  Trends Biochem Sci       Date:  2017-07-18       Impact factor: 13.807

4.  Goniometer-based femtosecond crystallography with X-ray free electron lasers.

Authors:  Aina E Cohen; S Michael Soltis; Ana González; Laura Aguila; Roberto Alonso-Mori; Christopher O Barnes; Elizabeth L Baxter; Winnie Brehmer; Aaron S Brewster; Axel T Brunger; Guillermo Calero; Joseph F Chang; Matthieu Chollet; Paul Ehrensberger; Thomas L Eriksson; Yiping Feng; Johan Hattne; Britt Hedman; Michael Hollenbeck; James M Holton; Stephen Keable; Brian K Kobilka; Elena G Kovaleva; Andrew C Kruse; Henrik T Lemke; Guowu Lin; Artem Y Lyubimov; Aashish Manglik; Irimpan I Mathews; Scott E McPhillips; Silke Nelson; John W Peters; Nicholas K Sauter; Clyde A Smith; Jinhu Song; Hilary P Stevenson; Yingssu Tsai; Monarin Uervirojnangkoorn; Vladimir Vinetsky; Soichi Wakatsuki; William I Weis; Oleg A Zadvornyy; Oliver B Zeldin; Diling Zhu; Keith O Hodgson
Journal:  Proc Natl Acad Sci U S A       Date:  2014-10-31       Impact factor: 11.205

5.  Expanding the femtosecond crystallography toolkit.

Authors:  Sol M Gruner
Journal:  Proc Natl Acad Sci U S A       Date:  2014-11-24       Impact factor: 11.205

6.  Dynamic Structural Biology Experiments at XFEL or Synchrotron Sources.

Authors:  Pierre Aller; Allen M Orville
Journal:  Methods Mol Biol       Date:  2021

7.  Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex.

Authors:  Artem Y Lyubimov; Monarin Uervirojnangkoorn; Oliver B Zeldin; Qiangjun Zhou; Minglei Zhao; Aaron S Brewster; Tara Michels-Clark; James M Holton; Nicholas K Sauter; William I Weis; Axel T Brunger
Journal:  Elife       Date:  2016-10-12       Impact factor: 8.140

Review 8.  Serial Femtosecond Crystallography of G Protein-Coupled Receptors.

Authors:  Benjamin Stauch; Vadim Cherezov
Journal:  Annu Rev Biophys       Date:  2018-03-15       Impact factor: 12.981

9.  Anaerobic fixed-target serial crystallography.

Authors:  Patrick Rabe; John H Beale; Agata Butryn; Pierre Aller; Anna Dirr; Pauline A Lang; Danny N Axford; Stephen B Carr; Thomas M Leissing; Michael A McDonough; Bradley Davy; Ali Ebrahim; Julien Orlans; Selina L S Storm; Allen M Orville; Christopher J Schofield; Robin L Owen
Journal:  IUCrJ       Date:  2020-08-21       Impact factor: 4.769

10.  Structure of the 3.3MDa, in vitro assembled, hubless bacteriophage T4 baseplate.

Authors:  Moh Lan Yap; Thomas Klose; Pavel Plevka; Anastasia Aksyuk; Xinzheng Zhang; Fumio Arisaka; Michael G Rossmann
Journal:  J Struct Biol       Date:  2014-07-03       Impact factor: 2.867

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