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Title: A revised partiality model and post-refinement algorithm for X-ray free-electron laser data

Abstract

An updated partiality model and post-refinement algorithm for XFEL snapshot diffraction data is presented and confirmed by observing anomalous density for S atoms at an X-ray wavelength of 1.3 Å. Research towards using X-ray free-electron laser (XFEL) data to solve structures using experimental phasing methods such as sulfur single-wavelength anomalous dispersion (SAD) has been hampered by shortcomings in the diffraction models for X-ray diffraction from FELs. Owing to errors in the orientation matrix and overly simple partiality models, researchers have required large numbers of images to converge to reliable estimates for the structure-factor amplitudes, which may not be feasible for all biological systems. Here, data for cytoplasmic polyhedrosis virus type 17 (CPV17) collected at 1.3 Å wavelength at the Linac Coherent Light Source (LCLS) are revisited. A previously published definition of a partiality model for reflections illuminated by self-amplified spontaneous emission (SASE) pulses is built upon, which defines a fraction between 0 and 1 based on the intersection of a reflection with a spread of Ewald spheres modelled by a super-Gaussian wavelength distribution in the X-ray beam. A method of post-refinement to refine the parameters of this model is suggested. This has generated a merged data set with an overallmore » discrepancy (by calculating the R{sub split} value) of 3.15% to 1.46 Å resolution from a 7225-image data set. The atomic numbers of C, N and O atoms in the structure are distinguishable in the electron-density map. There are 13 S atoms within the 237 residues of CPV17, excluding the initial disordered methionine. These only possess 0.42 anomalous scattering electrons each at 1.3 Å wavelength, but the 12 that have single predominant positions are easily detectable in the anomalous difference Fourier map. It is hoped that these improvements will lead towards XFEL experimental phase determination and structure determination by sulfur SAD and will generally increase the utility of the method for difficult cases.« less

Authors:
 [1]; ;  [2]; ;  [3];  [1];  [2];  [1]
  1. Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN (United Kingdom)
  2. Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 (United States)
  3. Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0QX (United Kingdom)
Publication Date:
OSTI Identifier:
22389069
Resource Type:
Journal Article
Journal Name:
Acta Crystallographica. Section D: Biological Crystallography
Additional Journal Information:
Journal Volume: 71; Journal Issue: Pt 6; Other Information: PMCID: PMC4461207; PMID: 26057680; PUBLISHER-ID: dz5368; OAI: oai:pubmedcentral.nih.gov:4461207; Copyright (c) Ginn et al. 2015; This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.; Country of input: International Atomic Energy Agency (IAEA); Journal ID: ISSN 0907-4449
Country of Publication:
Denmark
Language:
English
Subject:
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS; 75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; ALGORITHMS; AMPLITUDES; ATOMS; DENSITY; DISTRIBUTION; ELECTRON DENSITY; ELECTRONS; ERRORS; IMAGES; MATRICES; PULSES; SCATTERING; SPHERES; WAVELENGTHS

Citation Formats

Ginn, Helen Mary, Brewster, Aaron S., Hattne, Johan, Evans, Gwyndaf, Wagner, Armin, Grimes, Jonathan M., Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0QX, Sauter, Nicholas K., Sutton, Geoff, Stuart, David Ian, E-mail: dave@strubi.ox.ac.uk, and Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0QX. A revised partiality model and post-refinement algorithm for X-ray free-electron laser data. Denmark: N. p., 2015. Web. doi:10.1107/S1399004715006902.
Ginn, Helen Mary, Brewster, Aaron S., Hattne, Johan, Evans, Gwyndaf, Wagner, Armin, Grimes, Jonathan M., Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0QX, Sauter, Nicholas K., Sutton, Geoff, Stuart, David Ian, E-mail: dave@strubi.ox.ac.uk, & Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0QX. A revised partiality model and post-refinement algorithm for X-ray free-electron laser data. Denmark. https://doi.org/10.1107/S1399004715006902
Ginn, Helen Mary, Brewster, Aaron S., Hattne, Johan, Evans, Gwyndaf, Wagner, Armin, Grimes, Jonathan M., Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0QX, Sauter, Nicholas K., Sutton, Geoff, Stuart, David Ian, E-mail: dave@strubi.ox.ac.uk, and Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0QX. 2015. "A revised partiality model and post-refinement algorithm for X-ray free-electron laser data". Denmark. https://doi.org/10.1107/S1399004715006902.
@article{osti_22389069,
title = {A revised partiality model and post-refinement algorithm for X-ray free-electron laser data},
author = {Ginn, Helen Mary and Brewster, Aaron S. and Hattne, Johan and Evans, Gwyndaf and Wagner, Armin and Grimes, Jonathan M. and Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0QX and Sauter, Nicholas K. and Sutton, Geoff and Stuart, David Ian, E-mail: dave@strubi.ox.ac.uk and Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0QX},
abstractNote = {An updated partiality model and post-refinement algorithm for XFEL snapshot diffraction data is presented and confirmed by observing anomalous density for S atoms at an X-ray wavelength of 1.3 Å. Research towards using X-ray free-electron laser (XFEL) data to solve structures using experimental phasing methods such as sulfur single-wavelength anomalous dispersion (SAD) has been hampered by shortcomings in the diffraction models for X-ray diffraction from FELs. Owing to errors in the orientation matrix and overly simple partiality models, researchers have required large numbers of images to converge to reliable estimates for the structure-factor amplitudes, which may not be feasible for all biological systems. Here, data for cytoplasmic polyhedrosis virus type 17 (CPV17) collected at 1.3 Å wavelength at the Linac Coherent Light Source (LCLS) are revisited. A previously published definition of a partiality model for reflections illuminated by self-amplified spontaneous emission (SASE) pulses is built upon, which defines a fraction between 0 and 1 based on the intersection of a reflection with a spread of Ewald spheres modelled by a super-Gaussian wavelength distribution in the X-ray beam. A method of post-refinement to refine the parameters of this model is suggested. This has generated a merged data set with an overall discrepancy (by calculating the R{sub split} value) of 3.15% to 1.46 Å resolution from a 7225-image data set. The atomic numbers of C, N and O atoms in the structure are distinguishable in the electron-density map. There are 13 S atoms within the 237 residues of CPV17, excluding the initial disordered methionine. These only possess 0.42 anomalous scattering electrons each at 1.3 Å wavelength, but the 12 that have single predominant positions are easily detectable in the anomalous difference Fourier map. It is hoped that these improvements will lead towards XFEL experimental phase determination and structure determination by sulfur SAD and will generally increase the utility of the method for difficult cases.},
doi = {10.1107/S1399004715006902},
url = {https://www.osti.gov/biblio/22389069}, journal = {Acta Crystallographica. Section D: Biological Crystallography},
issn = {0907-4449},
number = Pt 6,
volume = 71,
place = {Denmark},
year = {2015},
month = {5}
}

Works referencing / citing this record:

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Linac Coherent Light Source: The first five years
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Resolving indexing ambiguities in X-ray free-electron laser diffraction patterns
journal, February 2019


X-ray Free Electron Laser Determination of Crystal Structures of Dark and Light States of a Reversibly Photoswitching Fluorescent Protein at Room Temperature
journal, September 2017


X-ray free electron laser: opportunities for drug discovery
journal, November 2017