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

Abstract

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 theR_splitvalue) 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 inmore » 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:

Ginn, Helen Mary ^[1]; Brewster, Aaron S. ^[2]; Hattne, Johan ^[2]; Evans, Gwyndaf ^[3]; Wagner, Armin ^[3]; Grimes, Jonathan M. ^[4]; Sauter, Nicholas K. ^[2]; Sutton, Geoff ^[1]; Stuart, David Ian ^[1]

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+ Show Author Affiliations

1. Wellcome Trust Centre for Human Genetics, Oxford (England)
2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
3. Harwell Science and Innovation Campus, Didcot (England)
4. Wellcome Trust Centre for Human Genetics, Oxford (England); Harwell Science and Innovation Campus, Didcot (England)

Publication Date:

Sat May 23 00:00:00 EDT 2015

Research Org.:

SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States)

Sponsoring Org.:

USDOE Office of Science (SC)

OSTI Identifier:

1188637

Grant/Contract Number:  

AC02-05CH11231

Resource Type:

Accepted Manuscript

Journal Name:

Acta Crystallographica. Section D: Biological Crystallography (Online)

Additional Journal Information:

Journal Name: Acta Crystallographica. Section D: Biological Crystallography (Online); Journal Volume: 71; Journal Issue: 6; Journal ID: ISSN 1399-0047

Publisher:

International Union of Crystallography

Country of Publication:

United States

Language:

English

Subject:

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; 59 BASIC BIOLOGICAL SCIENCES; post-refinement; free-electron laser; partiality