Literature DB >> 28628129

High-speed fixed-target serial virus crystallography.

Philip Roedig1, Helen M Ginn2,3, Tim Pakendorf1, Geoff Sutton2, Karl Harlos2, Thomas S Walter2, Jan Meyer1, Pontus Fischer1, Ramona Duman3, Ismo Vartiainen4, Bernd Reime1, Martin Warmer1, Aaron S Brewster5, Iris D Young5, Tara Michels-Clark5, Nicholas K Sauter5, Abhay Kotecha2, James Kelly6,7, David J Rowlands6, Marcin Sikorsky8, Silke Nelson8, Daniel S Damiani8, Roberto Alonso-Mori8, Jingshan Ren2, Elizabeth E Fry2, Christian David9, David I Stuart2,3, Armin Wagner3, Alke Meents1,10.   

Abstract

We report a method for serial X-ray crystallography at X-ray free-electron lasers (XFELs), which allows for full use of the current 120-Hz repetition rate of the Linear Coherent Light Source (LCLS). Using a micropatterned silicon chip in combination with the high-speed Roadrunner goniometer for sample delivery, we were able to determine the crystal structures of the picornavirus bovine enterovirus 2 (BEV2) and the cytoplasmic polyhedrosis virus type 18 polyhedrin, with total data collection times of less than 14 and 10 min, respectively. Our method requires only micrograms of sample and should therefore broaden the applicability of serial femtosecond crystallography to challenging projects for which only limited sample amounts are available. By synchronizing the sample exchange to the XFEL repetition rate, our method allows for most efficient use of the limited beam time available at XFELs and should enable a substantial increase in sample throughput at these facilities.

Entities:  

Mesh:

Year:  2017        PMID: 28628129      PMCID: PMC5588887          DOI: 10.1038/nmeth.4335

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


  53 in total

1.  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

2.  Measurement of the equilibrium relative humidity for common precipitant concentrations: facilitating controlled dehydration experiments.

Authors:  Matthew J Wheeler; Silvia Russi; Michael G Bowler; Matthew W Bowler
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2011-12-24

3.  Version 1.2 of the Crystallography and NMR system.

Authors:  Axel T Brunger
Journal:  Nat Protoc       Date:  2007       Impact factor: 13.491

Review 4.  Role of electrostatic repulsion in controlling pH-dependent conformational changes of viral fusion proteins.

Authors:  Joseph S Harrison; Chelsea D Higgins; Matthew J O'Meara; Jayne F Koellhoffer; Brian A Kuhlman; Jonathan R Lai
Journal:  Structure       Date:  2013-07-02       Impact factor: 5.006

5.  Bovine enterovirus 2: complete genomic sequence and molecular modelling of a reference strain and a wild-type isolate from endemically infected US cattle.

Authors:  S D Goens; S Botero; A Zemla; C Ecale Zhou; M L Perdue
Journal:  J Gen Virol       Date:  2004-11       Impact factor: 3.891

6.  Fixed-target protein serial microcrystallography with an x-ray free electron laser.

Authors:  Mark S Hunter; Brent Segelke; Marc Messerschmidt; Garth J Williams; Nadia A Zatsepin; Anton Barty; W Henry Benner; David B Carlson; Matthew Coleman; Alexander Graf; Stefan P Hau-Riege; Tommaso Pardini; M Marvin Seibert; James Evans; Sébastien Boutet; Matthias Frank
Journal:  Sci Rep       Date:  2014-08-12       Impact factor: 4.379

7.  Macromolecular diffractive imaging using imperfect crystals.

Authors:  Kartik Ayyer; Oleksandr M Yefanov; Dominik Oberthür; Shatabdi Roy-Chowdhury; Lorenzo Galli; Valerio Mariani; Shibom Basu; Jesse Coe; Chelsie E Conrad; Raimund Fromme; Alexander Schaffer; Katerina Dörner; Daniel James; Christopher Kupitz; Markus Metz; Garrett Nelson; Paulraj Lourdu Xavier; Kenneth R Beyerlein; Marius Schmidt; Iosifina Sarrou; John C H Spence; Uwe Weierstall; Thomas A White; Jay-How Yang; Yun Zhao; Mengning Liang; Andrew Aquila; Mark S Hunter; Joseph S Robinson; Jason E Koglin; Sébastien Boutet; Petra Fromme; Anton Barty; Henry N Chapman
Journal:  Nature       Date:  2016-02-11       Impact factor: 49.962

8.  High-density grids for efficient data collection from multiple crystals.

Authors:  Elizabeth L Baxter; Laura Aguila; Roberto Alonso-Mori; Christopher O Barnes; Christopher A Bonagura; Winnie Brehmer; Axel T Brunger; Guillermo Calero; Tom T Caradoc-Davies; Ruchira Chatterjee; William F Degrado; James S Fraser; Mohamed Ibrahim; Jan Kern; Brian K Kobilka; Andrew C Kruse; Karl M Larsson; Heinrik T Lemke; Artem Y Lyubimov; Aashish Manglik; Scott E McPhillips; Erik Norgren; Siew S Pang; S M Soltis; Jinhu Song; Jessica Thomaston; Yingssu Tsai; William I Weis; Rahel A Woldeyes; Vittal Yachandra; Junko Yano; Athina Zouni; Aina E Cohen
Journal:  Acta Crystallogr D Struct Biol       Date:  2016-01-01       Impact factor: 7.652

9.  Polyhedra structures and the evolution of the insect viruses.

Authors:  Xiaoyun Ji; Danny Axford; Robin Owen; Gwyndaf Evans; Helen M Ginn; Geoff Sutton; David I Stuart
Journal:  J Struct Biol       Date:  2015-08-18       Impact factor: 2.867

10.  A high-transparency, micro-patternable chip for X-ray diffraction analysis of microcrystals under native growth conditions.

Authors:  Thomas D Murray; Artem Y Lyubimov; Craig M Ogata; Huy Vo; Monarin Uervirojnangkoorn; Axel T Brunger; James M Berger
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2015-09-26
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  49 in total

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

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

2.  Structural biology: doors open at the European XFEL.

Authors:  Vivien Marx
Journal:  Nat Methods       Date:  2017-08-31       Impact factor: 28.547

Review 3.  An outlook on using serial femtosecond crystallography in drug discovery.

Authors:  Alexey Mishin; Anastasiia Gusach; Aleksandra Luginina; Egor Marin; Valentin Borshchevskiy; Vadim Cherezov
Journal:  Expert Opin Drug Discov       Date:  2019-06-11       Impact factor: 6.098

4.  3D printed droplet generation devices for serial femtosecond crystallography enabled by surface coating.

Authors:  Austin Echelmeier; Daihyun Kim; Jorvani Cruz Villarreal; Jesse Coe; Sebastian Quintana; Gerrit Brehm; Ana Egatz-Gomez; Reza Nazari; Raymond G Sierra; Jason E Koglin; Alexander Batyuk; Mark S Hunter; Sébastien Boutet; Nadia Zatsepin; Richard A Kirian; Thomas D Grant; Petra Fromme; Alexandra Ros
Journal:  J Appl Crystallogr       Date:  2019-08-29       Impact factor: 3.304

5.  Co-crystal structure of the Fusobacterium ulcerans ZTP riboswitch using an X-ray free-electron laser.

Authors:  Christopher Jones; Brandon Tran; Chelsie Conrad; Jason Stagno; Robert Trachman; Pontus Fischer; Alke Meents; Adrian Ferré-D'Amaré
Journal:  Acta Crystallogr F Struct Biol Commun       Date:  2019-06-28       Impact factor: 1.056

Review 6.  The complementarity of serial femtosecond crystallography and MicroED for structure determination from microcrystals.

Authors:  Nadia A Zatsepin; Chufeng Li; Paige Colasurd; Brent L Nannenga
Journal:  Curr Opin Struct Biol       Date:  2019-07-22       Impact factor: 6.809

7.  Co-crystal structure of the iMango-III fluorescent RNA aptamer using an X-ray free-electron laser.

Authors:  Robert J Trachman; Jason R Stagno; Chelsie Conrad; Christopher P Jones; Pontus Fischer; Alke Meents; Yun Xing Wang; Adrian R Ferré-D'Amaré
Journal:  Acta Crystallogr F Struct Biol Commun       Date:  2019-08-02       Impact factor: 1.056

8.  Room-temperature serial synchrotron crystallography of Drosophila cryptochrome.

Authors:  Connor M Schneps; Abir Ganguly; Brian R Crane
Journal:  Acta Crystallogr D Struct Biol       Date:  2022-07-27       Impact factor: 5.699

9.  Fixed-target serial femtosecond crystallography using in cellulo grown microcrystals.

Authors:  J Mia Lahey-Rudolph; Robert Schönherr; Miriam Barthelmess; Pontus Fischer; Carolin Seuring; Armin Wagner; Alke Meents; Lars Redecke
Journal:  IUCrJ       Date:  2021-06-18       Impact factor: 4.769

10.  Polyimide mesh-based sample holder with irregular crystal mounting holes for fixed-target serial crystallography.

Authors:  Ki Hyun Nam; Jihan Kim; Yunje Cho
Journal:  Sci Rep       Date:  2021-06-23       Impact factor: 4.379

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