Literature DB >> 27487825

Fixed target combined with spectral mapping: approaching 100% hit rates for serial crystallography.

Saeed Oghbaey1, Antoine Sarracini1, Helen M Ginn2, Olivier Pare-Labrosse1, Anling Kuo3, Alexander Marx4, Sascha W Epp4, Darren A Sherrell5, Bryan T Eger3, Yinpeng Zhong4, Rolf Loch4, Valerio Mariani6, Roberto Alonso-Mori7, Silke Nelson7, Henrik T Lemke7, Robin L Owen5, Arwen R Pearson8, David I Stuart2, Oliver P Ernst3, Henrike M Mueller-Werkmeister1, R J Dwayne Miller1.   

Abstract

The advent of ultrafast highly brilliant coherent X-ray free-electron laser sources has driven the development of novel structure-determination approaches for proteins, and promises visualization of protein dynamics on sub-picosecond timescales with full atomic resolution. Significant efforts are being applied to the development of sample-delivery systems that allow these unique sources to be most efficiently exploited for high-throughput serial femtosecond crystallography. Here, the next iteration of a fixed-target crystallography chip designed for rapid and reliable delivery of up to 11 259 protein crystals with high spatial precision is presented. An experimental scheme for predetermining the positions of crystals in the chip by means of in situ spectroscopy using a fiducial system for rapid, precise alignment and registration of the crystal positions is presented. This delivers unprecedented performance in serial crystallography experiments at room temperature under atmospheric pressure, giving a raw hit rate approaching 100% with an effective indexing rate of approximately 50%, increasing the efficiency of beam usage and allowing the method to be applied to systems where the number of crystals is limited.

Entities:  

Keywords:  femtosecond time-resolved crystallography; fixed-target sample delivery; high-throughput serial crystallography; room-temperature crystallography

Mesh:

Substances:

Year:  2016        PMID: 27487825      PMCID: PMC5937680          DOI: 10.1107/S2059798316010834

Source DB:  PubMed          Journal:  Acta Crystallogr D Struct Biol        ISSN: 2059-7983            Impact factor:   7.652


  34 in total

1.  The RATIO method for time-resolved Laue crystallography.

Authors:  Philip Coppens; Mateusz Pitak; Milan Gembicky; Marc Messerschmidt; Stephan Scheins; Jason Benedict; Shin Ichi Adachi; Tokushi Sato; Shunsuke Nozawa; Kohei Ichiyanagi; Matthieu Chollet; Shin Ya Koshihara
Journal:  J Synchrotron Radiat       Date:  2009-01-10       Impact factor: 2.616

2.  Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography.

Authors:  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; 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
Journal:  Nat Commun       Date:  2014       Impact factor: 14.919

3.  Features and development of Coot.

Authors:  P Emsley; B Lohkamp; W G Scott; K Cowtan
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-03-24

4.  Revealing low-dose radiation damage using single-crystal spectroscopy.

Authors:  Robin L Owen; Briony A Yorke; James A Gowdy; Arwen R Pearson
Journal:  J Synchrotron Radiat       Date:  2011-03-19       Impact factor: 2.616

5.  REFMAC5 for the refinement of macromolecular crystal structures.

Authors:  Garib N Murshudov; Pavol Skubák; Andrey A Lebedev; Navraj S Pannu; Roberto A Steiner; Robert A Nicholls; Martyn D Winn; Fei Long; Alexei A Vagin
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2011-03-18

6.  Overview of the CCP4 suite and current developments.

Authors:  Martyn D Winn; Charles C Ballard; Kevin D Cowtan; Eleanor J Dodson; Paul Emsley; Phil R Evans; Ronan M Keegan; Eugene B Krissinel; Andrew G W Leslie; Airlie McCoy; Stuart J McNicholas; Garib N Murshudov; Navraj S Pannu; Elizabeth A Potterton; Harold R Powell; Randy J Read; Alexei Vagin; Keith S Wilson
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2011-03-18

7.  Structure of CPV17 polyhedrin determined by the improved analysis of serial femtosecond crystallographic data.

Authors:  Helen M Ginn; Marc Messerschmidt; Xiaoyun Ji; Hanwen Zhang; Danny Axford; Richard J Gildea; Graeme Winter; Aaron S Brewster; Johan Hattne; Armin Wagner; Jonathan M Grimes; Gwyndaf Evans; Nicholas K Sauter; Geoff Sutton; David I Stuart
Journal:  Nat Commun       Date:  2015-03-09       Impact factor: 14.919

8.  Capture and X-ray diffraction studies of protein microcrystals in a microfluidic trap array.

Authors:  Artem Y Lyubimov; Thomas D Murray; Antoine Koehl; Ismail Emre Araci; Monarin Uervirojnangkoorn; Oliver B Zeldin; Aina E Cohen; S Michael Soltis; Elizabeth L Baxter; Aaron S Brewster; Nicholas K Sauter; Axel T Brunger; James M Berger
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2015-03-27

9.  Diffraction-geometry refinement in the DIALS framework.

Authors:  David G Waterman; Graeme Winter; Richard J Gildea; James M Parkhurst; Aaron S Brewster; Nicholas K Sauter; Gwyndaf Evans
Journal:  Acta Crystallogr D Struct Biol       Date:  2016-03-30       Impact factor: 7.652

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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  21 in total

1.  Crystal-on-crystal chips for in situ serial diffraction at room temperature.

Authors:  Zhong Ren; Medine Ayhan; Sepalika Bandara; Kalinga Bowatte; Indika Kumarapperuma; Semini Gunawardana; Heewhan Shin; Cong Wang; Xiaoli Zeng; Xiaojing Yang
Journal:  Lab Chip       Date:  2018-07-24       Impact factor: 6.799

2.  DIY XES - development of an inexpensive, versatile, and easy to fabricate XES analyzer and sample delivery system.

Authors:  Scott C Jensen; Brendan Sullivan; Daniel A Hartzler; Yulia Pushkar
Journal:  Xray Spectrom       Date:  2019-02-13       Impact factor: 1.488

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

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

4.  High-throughput in situ X-ray screening of and data collection from protein crystals at room temperature and under cryogenic conditions.

Authors:  Jana Broecker; Takefumi Morizumi; Wei-Lin Ou; Viviane Klingel; Anling Kuo; David J Kissick; Andrii Ishchenko; Ming-Yue Lee; Shenglan Xu; Oleg Makarov; Vadim Cherezov; Craig M Ogata; Oliver P Ernst
Journal:  Nat Protoc       Date:  2018-01-04       Impact factor: 13.491

5.  Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers.

Authors:  Franklin D Fuller; Sheraz Gul; Ruchira Chatterjee; E Sethe Burgie; Iris D Young; Hugo Lebrette; Vivek Srinivas; Aaron S Brewster; Tara Michels-Clark; Jonathan A Clinger; Babak Andi; Mohamed Ibrahim; Ernest Pastor; Casper de Lichtenberg; Rana Hussein; Christopher J Pollock; Miao Zhang; Claudiu A Stan; Thomas Kroll; Thomas Fransson; Clemens Weninger; Markus Kubin; Pierre Aller; Louise Lassalle; Philipp Bräuer; Mitchell D Miller; Muhamed Amin; Sergey Koroidov; Christian G Roessler; Marc Allaire; Raymond G Sierra; Peter T Docker; James M Glownia; Silke Nelson; Jason E Koglin; Diling Zhu; Matthieu Chollet; Sanghoon Song; Henrik Lemke; Mengning Liang; Dimosthenis Sokaras; Roberto Alonso-Mori; Athina Zouni; Johannes Messinger; Uwe Bergmann; Amie K Boal; J Martin Bollinger; Carsten Krebs; Martin Högbom; George N Phillips; Richard D Vierstra; Nicholas K Sauter; Allen M Orville; Jan Kern; Vittal K Yachandra; Junko Yano
Journal:  Nat Methods       Date:  2017-02-27       Impact factor: 28.547

6.  Plug-and-play polymer microfluidic chips for hydrated, room temperature, fixed-target serial crystallography.

Authors:  Deepshika Gilbile; Megan L Shelby; Artem Y Lyubimov; Jennifer L Wierman; Diana C F Monteiro; Aina E Cohen; Silvia Russi; Matthew A Coleman; Matthias Frank; Tonya L Kuhl
Journal:  Lab Chip       Date:  2021-12-07       Impact factor: 7.517

7.  High-speed fixed-target serial virus crystallography.

Authors:  Philip Roedig; Helen M Ginn; Tim Pakendorf; Geoff Sutton; Karl Harlos; Thomas S Walter; Jan Meyer; Pontus Fischer; Ramona Duman; Ismo Vartiainen; Bernd Reime; Martin Warmer; Aaron S Brewster; Iris D Young; Tara Michels-Clark; Nicholas K Sauter; Abhay Kotecha; James Kelly; David J Rowlands; Marcin Sikorsky; Silke Nelson; Daniel S Damiani; Roberto Alonso-Mori; Jingshan Ren; Elizabeth E Fry; Christian David; David I Stuart; Armin Wagner; Alke Meents
Journal:  Nat Methods       Date:  2017-06-19       Impact factor: 28.547

8.  Mixing injector enables time-resolved crystallography with high hit rate at X-ray free electron lasers.

Authors:  George D Calvey; Andrea M Katz; Chris B Schaffer; Lois Pollack
Journal:  Struct Dyn       Date:  2016-08-29       Impact factor: 2.920

9.  Towards a compact and precise sample holder for macromolecular crystallography.

Authors:  Gergely Papp; Christopher Rossi; Robert Janocha; Clement Sorez; Marcos Lopez-Marrero; Anthony Astruc; Andrew McCarthy; Hassan Belrhali; Matthew W Bowler; Florent Cipriani
Journal:  Acta Crystallogr D Struct Biol       Date:  2017-09-29       Impact factor: 7.652

10.  Hierarchical clustering for multiple-crystal macromolecular crystallography experiments: the ccCluster program.

Authors:  Gianluca Santoni; Ulrich Zander; Christoph Mueller-Dieckmann; Gordon Leonard; Alexander Popov
Journal:  J Appl Crystallogr       Date:  2017-11-29       Impact factor: 3.304

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