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Title: High-speed fixed-target serial virus crystallography

Abstract

Here, 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.

Authors:
 [1];  [2];  [1];  [3];  [3];  [3];  [1];  [1];  [4];  [5];  [1];  [1];  [6]; ORCiD logo [6];  [6];  [6];  [3];  [7];  [8];  [9] more »;  [9];  [9]; ORCiD logo [9];  [3];  [3];  [10]; ORCiD logo [2];  [4];  [11] « less
+ Show Author Affiliations
  1. Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany). Photon Science
  2. Univ. of Oxford (United Kingdom). Division of Structural Biology, Wellcome Trust Centre for Human Genetics; Science and Technology Facilities Council (STFC), Harwell Campus, Oxford (United Kingdom). Diamond Light Source, Ltd.
  3. Univ. of Oxford (United Kingdom). Division of Structural Biology, Wellcome Trust Centre for Human Genetics
  4. Science and Technology Facilities Council (STFC), Harwell Campus, Oxford (United Kingdom). Diamond Light Source, Ltd.
  5. Univ. of Eastern Finland, Joensuu (Finland). Inst. of Photonics
  6. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrated Bioimaging Division
  7. Univ. of Leeds (United Kingdom). School of Molecular and Cellular Biology; Pirbright Inst., Pirbright (United Kingdom)
  8. Univ. of Leeds (United Kingdom). School of Molecular and Cellular Biology
  9. SLAC National Accelerator Lab., Menlo Park, CA (United States). Linac Coherent Light Source (LCLS)
  10. Paul Scherrer Inst. (PSI), Villigen (Switzerland)
  11. Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany). Photon Science; Center for Free Electron Laser Science (CFEL), Hamburg (Germany)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES); National Institutes of Health (NIH); Wellcome Trust
OSTI Identifier:
1421803
Grant/Contract Number:  
AC02-05CH11231; AC02-76SF00515; MR/N00065X/1; GM102520; GM117126
Resource Type:
Accepted Manuscript
Journal Name:
Nature Methods
Additional Journal Information:
Journal Volume: 14; Journal Issue: 8; Journal ID: ISSN 1548-7091
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Nanocrystallography; Proteins; Virology

Citation Formats

Roedig, Philip, Ginn, Helen M., Pakendorf, Tim, Sutton, Geoff, Harlos, Karl, Walter, Thomas S., Meyer, Jan, Fischer, Pontus, Duman, Ramona, Vartiainen, Ismo, Reime, Bernd, Warmer, Martin, Brewster, Aaron S., Young, Iris D., Michels-Clark, Tara, Sauter, Nicholas K., Kotecha, Abhay, Kelly, James, Rowlands, David J., Sikorsky, Marcin, Nelson, Silke, Damiani, Daniel S., Alonso-Mori, Roberto, Ren, Jingshan, Fry, Elizabeth E., David, Christian, Stuart, David I., Wagner, Armin, and Meents, Alke. High-speed fixed-target serial virus crystallography. United States: N. p., 2017. Web. doi:10.1038/nmeth.4335.
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Roedig, Philip, Ginn, Helen M., Pakendorf, Tim, Sutton, Geoff, Harlos, Karl, Walter, Thomas S., Meyer, Jan, Fischer, Pontus, Duman, Ramona, Vartiainen, Ismo, Reime, Bernd, Warmer, Martin, Brewster, Aaron S., Young, Iris D., Michels-Clark, Tara, Sauter, Nicholas K., Kotecha, Abhay, Kelly, James, Rowlands, David J., Sikorsky, Marcin, Nelson, Silke, Damiani, Daniel S., Alonso-Mori, Roberto, Ren, Jingshan, Fry, Elizabeth E., David, Christian, Stuart, David I., Wagner, Armin, & Meents, Alke. High-speed fixed-target serial virus crystallography. United States. https://doi.org/10.1038/nmeth.4335
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Roedig, Philip, Ginn, Helen M., Pakendorf, Tim, Sutton, Geoff, Harlos, Karl, Walter, Thomas S., Meyer, Jan, Fischer, Pontus, Duman, Ramona, Vartiainen, Ismo, Reime, Bernd, Warmer, Martin, Brewster, Aaron S., Young, Iris D., Michels-Clark, Tara, Sauter, Nicholas K., Kotecha, Abhay, Kelly, James, Rowlands, David J., Sikorsky, Marcin, Nelson, Silke, Damiani, Daniel S., Alonso-Mori, Roberto, Ren, Jingshan, Fry, Elizabeth E., David, Christian, Stuart, David I., Wagner, Armin, and Meents, Alke. Mon . "High-speed fixed-target serial virus crystallography". United States. https://doi.org/10.1038/nmeth.4335. https://www.osti.gov/servlets/purl/1421803.
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@article{osti_1421803,
title = {High-speed fixed-target serial virus crystallography},
author = {Roedig, Philip and Ginn, Helen M. and Pakendorf, Tim and Sutton, Geoff and Harlos, Karl and Walter, Thomas S. and Meyer, Jan and Fischer, Pontus and Duman, Ramona and Vartiainen, Ismo and Reime, Bernd and Warmer, Martin and Brewster, Aaron S. and Young, Iris D. and Michels-Clark, Tara and Sauter, Nicholas K. and Kotecha, Abhay and Kelly, James and Rowlands, David J. and Sikorsky, Marcin and Nelson, Silke and Damiani, Daniel S. and Alonso-Mori, Roberto and Ren, Jingshan and Fry, Elizabeth E. and David, Christian and Stuart, David I. and Wagner, Armin and Meents, Alke},
abstractNote = {Here, 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.},
doi = {10.1038/nmeth.4335},
journal = {Nature Methods},
number = 8,
volume = 14,
place = {United States},
year = {Mon Jun 19 00:00:00 EDT 2017},
month = {Mon Jun 19 00:00:00 EDT 2017}
}
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    • Knoška, Juraj; Adriano, Luigi; Awel, Salah
    • Deutsches Elektronen-Synchrotron, DESY, Hamburg
    • DOI: 10.3204/pubdb-2020-00687

    Perspective: Opportunities for ultrafast science at SwissFEL
    text, January 2017

    Strategies for sample delivery for femtosecond crystallography
    text, January 2019

    The Single Particles, Clusters and Biomolecules and Serial Femtosecond Crystallography instrument of the European XFEL: initial installation
    text, January 2019

    • Mancuso, Adrian P.; Aquila, Andrew; Batchelor, Lewis
    • Deutsches Elektronen-Synchrotron, DESY, Hamburg
    • DOI: 10.3204/pubdb-2019-01957

    On-chip crystallization for serial crystallography experiments and on-chip ligand-binding studies
    text, January 2019

    • Lieske, Julia; Cerv, Maximilian; Kreida, Stefan
    • Deutsches Elektronen-Synchrotron, DESY, Hamburg
    • DOI: 10.3204/pubdb-2019-02620

    Co-crystal structure of the Fusobacterium ulcerans ZTP riboswitch using an X-ray free-electron laser
    text, January 2019

    • Jones, Christopher; Tran, Brandon; Conrad, Chelsie
    • Deutsches Elektronen-Synchrotron, DESY, Hamburg
    • DOI: 10.3204/pubdb-2019-02740

    Protein phase separation and determinants of in cell crystallization
    text, January 2019

    • Mudogo, Celestin Nzanzu; Falke, Sven; Brognaro dos Santos, Hevila
    • Deutsches Elektronen-Synchrotron, DESY, Hamburg
    • DOI: 10.3204/pubdb-2020-00138

    Ultracompact 3D microfluidics for time-resolved structural biology
    text, January 2020

    • Knoska, Juraj; Adriano, Luigi; Awel, Salah
    • Deutsches Elektronen-Synchrotron, DESY, Hamburg
    • DOI: 10.3204/pubdb-2020-00623

    Perspective: Opportunities for ultrafast science at SwissFEL
    text, January 2017

    Stimulated transitions in resonant atom Majorana mixing
    text, January 2017

    Multi-wavelength anomalous diffraction de novo phasing using a two-colour X-ray free-electron laser with wide tunability
    journal, October 2017

    Towards in cellulo virus crystallography
    journal, February 2018

    Lard Injection Matrix for Serial Crystallography
    journal, August 2020

    • Nam, Ki Hyun
    • International Journal of Molecular Sciences, Vol. 21, Issue 17
    • DOI: 10.3390/ijms21175977

    Perspective: Opportunities for ultrafast science at SwissFEL
    text, January 2017

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