skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals

Abstract

There is considerable potential for X-ray free electron lasers (XFELs) to enable determination of macromolecular crystal structures that are difficult to solve using current synchrotron sources. Prior XFEL studies often involved the collection of thousands to millions of diffraction images, in part due to limitations of data processing methods. We implemented a data processing system based on classical post-refinement techniques, adapted to specific properties of XFEL diffraction data. When applied to XFEL data from three different proteins collected using various sample delivery systems and XFEL beam parameters, our method improved the quality of the diffraction data as well as the resulting refined atomic models and electron density maps. Moreover, the number of observations for a reflection necessary to assemble an accurate data set could be reduced to a few observations. These developments will help expand the applicability of XFEL crystallography to challenging biological systems, including cases where sample is limited.

Authors:
 [1];  [1];  [1]; ORCiD logo [2];  [3];  [3]; ORCiD logo [4]; ORCiD logo [5]
  1. Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States
  2. Janelia Research Campus, Ashburn, United States
  3. Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States
  4. Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States, Department of Neurology and Neurological Sciences, Howard Hughes Medical Institute, Stanford University, Stanford, United States, Department of Photon Science, Stanford University, Stanford, United States
  5. Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States, Department of Photon Science, Stanford University, Stanford, United States, Department of Structural Biology, Stanford University, Stanford, United States
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1184051
Alternate Identifier(s):
OSTI ID: 1209798; OSTI ID: 1257268; OSTI ID: 1512179
Grant/Contract Number:  
AC02-05CH11231; GM103393; GM095887; GM102520
Resource Type:
Journal Article: Published Article
Journal Name:
eLife
Additional Journal Information:
Journal Name: eLife Journal Volume: 4; Journal ID: ISSN 2050-084X
Publisher:
eLife Sciences Publications, Ltd.
Country of Publication:
United States
Language:
English
Subject:
36 MATERIALS SCIENCE; 59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Uervirojnangkoorn, Monarin, Zeldin, Oliver B., Lyubimov, Artem Y., Hattne, Johan, Brewster, Aaron S., Sauter, Nicholas K., Brunger, Axel T., and Weis, William I. Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals. United States: N. p., 2015. Web. doi:10.7554/eLife.05421.
Uervirojnangkoorn, Monarin, Zeldin, Oliver B., Lyubimov, Artem Y., Hattne, Johan, Brewster, Aaron S., Sauter, Nicholas K., Brunger, Axel T., & Weis, William I. Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals. United States. https://doi.org/10.7554/eLife.05421
Uervirojnangkoorn, Monarin, Zeldin, Oliver B., Lyubimov, Artem Y., Hattne, Johan, Brewster, Aaron S., Sauter, Nicholas K., Brunger, Axel T., and Weis, William I. 2015. "Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals". United States. https://doi.org/10.7554/eLife.05421.
@article{osti_1184051,
title = {Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals},
author = {Uervirojnangkoorn, Monarin and Zeldin, Oliver B. and Lyubimov, Artem Y. and Hattne, Johan and Brewster, Aaron S. and Sauter, Nicholas K. and Brunger, Axel T. and Weis, William I.},
abstractNote = {There is considerable potential for X-ray free electron lasers (XFELs) to enable determination of macromolecular crystal structures that are difficult to solve using current synchrotron sources. Prior XFEL studies often involved the collection of thousands to millions of diffraction images, in part due to limitations of data processing methods. We implemented a data processing system based on classical post-refinement techniques, adapted to specific properties of XFEL diffraction data. When applied to XFEL data from three different proteins collected using various sample delivery systems and XFEL beam parameters, our method improved the quality of the diffraction data as well as the resulting refined atomic models and electron density maps. Moreover, the number of observations for a reflection necessary to assemble an accurate data set could be reduced to a few observations. These developments will help expand the applicability of XFEL crystallography to challenging biological systems, including cases where sample is limited.},
doi = {10.7554/eLife.05421},
url = {https://www.osti.gov/biblio/1184051}, journal = {eLife},
issn = {2050-084X},
number = ,
volume = 4,
place = {United States},
year = {Tue Mar 17 00:00:00 EDT 2015},
month = {Tue Mar 17 00:00:00 EDT 2015}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at https://doi.org/10.7554/eLife.05421

Citation Metrics:
Cited by: 86 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Goniometer-based femtosecond crystallography with X-ray free electron lasers
journal, October 2014


Processing and post-refinement of oscillation camera data
journal, December 1979


Overview of the CCP 4 suite and current developments
journal, March 2011


Changes to crystals of Escherichia coli β-galactosidase during room-temperature/low-temperature cycling and their relation to cryo-annealing
journal, October 2007


Radiation damage in macromolecular crystallography: what is it and why should we care?
journal, March 2010


Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography
journal, February 2014


MolProbity : all-atom structure validation for macromolecular crystallography
journal, December 2009


Features and development of Coot
journal, March 2010


New Python-based methods for data processing
journal, June 2013


Processing of X-ray snapshots from crystals in random orientations
journal, July 2014


Demonstration of self-seeding in a hard-X-ray free-electron laser
journal, August 2012


Structure of CPV17 polyhedrin determined by the improved analysis of serial femtosecond crystallographic data
journal, March 2015


Femtosecond protein nanocrystallography—data analysis methods
journal, January 2010


Matching X-ray beam and detector properties to protein crystals of different perfection
journal, March 2014


Towards automated crystallographic structure refinement with phenix.refine
journal, March 2012


The oscillation method for crystals with very large unit cells
journal, November 1979


PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010


Imaging biological specimens with high-intensity soft x rays
journal, January 1986


A single-shot transmissive spectrometer for hard x-ray free electron lasers
journal, July 2012


Predicting the X-ray lifetime of protein crystals
journal, December 2013


A Description of Imperfections in Protein Crystals
journal, September 1998


XFEL diffraction: developing processing methods to optimize data quality
journal, January 2015


Structural analysis of zinc substitutions in the active site of thermolysin
journal, October 1995


Collective instabilities and high-gain regime in a free electron laser
journal, July 1984


The Computational Crystallography Toolbox : crystallographic algorithms in a reusable software framework
journal, January 2002


Improved crystal orientation and physical properties from single-shot XFEL stills
journal, November 2014


Automated diffraction image analysis and spot searching for high-throughput crystal screening
journal, January 2006


Determination of damage-free crystal structure of an X-ray–sensitive protein using an XFEL
journal, May 2014


Potential for biomolecular imaging with femtosecond X-ray pulses
journal, August 2000


Python for Scientific Computing
journal, January 2007


Macromolecular crystallography with synchrotron radiation: photographic data collection and polarization correction
journal, June 1982


Post-refinement method for snapshot serial crystallography
journal, July 2014


Gas dynamic virtual nozzle for generation of microscopic droplet streams
journal, September 2008


Phaser crystallographic software
journal, July 2007


Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers
journal, March 2014


Crystallographic model quality at a glance
journal, February 2009


Better models by discarding data?
journal, June 2013


Nanoflow electrospinning serial femtosecond crystallography
journal, October 2012