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Title: Indexing amyloid peptide diffraction from serial femtosecond crystallography: new algorithms for sparse patterns

Abstract

Special methods are required to interpret sparse diffraction patterns collected from peptide crystals at X-ray free-electron lasers. Bragg spots can be indexed from composite-image powder rings, with crystal orientations then deduced from a very limited number of spot positions. Still diffraction patterns from peptide nanocrystals with small unit cells are challenging to index using conventional methods owing to the limited number of spots and the lack of crystal orientation information for individual images. New indexing algorithms have been developed as part of the Computational Crystallography Toolbox (cctbx) to overcome these challenges. Accurate unit-cell information derived from an aggregate data set from thousands of diffraction patterns can be used to determine a crystal orientation matrix for individual images with as few as five reflections. These algorithms are potentially applicable not only to amyloid peptides but also to any set of diffraction patterns with sparse properties, such as low-resolution virus structures or high-throughput screening of still images captured by raster-scanning at synchrotron sources. As a proof of concept for this technique, successful integration of X-ray free-electron laser (XFEL) data to 2.5 Å resolution for the amyloid segment GNNQQNY from the Sup35 yeast prion is presented.

Authors:
 [1];  [2];  [3];  [3];  [2];  [3]; ;  [1];  [2];  [3];  [2];  [3];  [3];  [1];  [3];  [2];  [3];  [3];  [1]
  1. Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States)
  2. University of California, Los Angeles, CA 90095-1570 (United States)
  3. (United States)
Publication Date:
OSTI Identifier:
22347713
Resource Type:
Journal Article
Resource Relation:
Journal Name: Acta Crystallographica. Section D: Biological Crystallography; Journal Volume: 71; Journal Issue: Pt 2; Other Information: PMCID: PMC4321489; PMID: 25664747; PUBLISHER-ID: dz5348; OAI: oai:pubmedcentral.nih.gov:4321489; Copyright (c) Brewster 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)
Country of Publication:
Denmark
Language:
English
Subject:
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; ALGORITHMS; CRYSTALLOGRAPHY; CRYSTALS; DIFFRACTION; ELECTRONS; IMAGES; INDEXES; MATRICES; ORIENTATION; POWDERS; REFLECTION; RESOLUTION; RINGS; SCREENING

Citation Formats

Brewster, Aaron S., Sawaya, Michael R., University of California, Los Angeles, CA 90095-1570, University of California, Los Angeles, CA 90095-1570, Rodriguez, Jose, University of California, Los Angeles, CA 90095-1570, Hattne, Johan, Echols, Nathaniel, McFarlane, Heather T., University of California, Los Angeles, CA 90095-1570, Cascio, Duilio, University of California, Los Angeles, CA 90095-1570, University of California, Los Angeles, CA 90095-1570, Adams, Paul D., University of California, Berkeley, CA 94720, Eisenberg, David S., University of California, Los Angeles, CA 90095-1570, University of California, Los Angeles, CA 90095-1570, and Sauter, Nicholas K., E-mail: nksauter@lbl.gov. Indexing amyloid peptide diffraction from serial femtosecond crystallography: new algorithms for sparse patterns. Denmark: N. p., 2015. Web. doi:10.1107/S1399004714026145.
Brewster, Aaron S., Sawaya, Michael R., University of California, Los Angeles, CA 90095-1570, University of California, Los Angeles, CA 90095-1570, Rodriguez, Jose, University of California, Los Angeles, CA 90095-1570, Hattne, Johan, Echols, Nathaniel, McFarlane, Heather T., University of California, Los Angeles, CA 90095-1570, Cascio, Duilio, University of California, Los Angeles, CA 90095-1570, University of California, Los Angeles, CA 90095-1570, Adams, Paul D., University of California, Berkeley, CA 94720, Eisenberg, David S., University of California, Los Angeles, CA 90095-1570, University of California, Los Angeles, CA 90095-1570, & Sauter, Nicholas K., E-mail: nksauter@lbl.gov. Indexing amyloid peptide diffraction from serial femtosecond crystallography: new algorithms for sparse patterns. Denmark. doi:10.1107/S1399004714026145.
Brewster, Aaron S., Sawaya, Michael R., University of California, Los Angeles, CA 90095-1570, University of California, Los Angeles, CA 90095-1570, Rodriguez, Jose, University of California, Los Angeles, CA 90095-1570, Hattne, Johan, Echols, Nathaniel, McFarlane, Heather T., University of California, Los Angeles, CA 90095-1570, Cascio, Duilio, University of California, Los Angeles, CA 90095-1570, University of California, Los Angeles, CA 90095-1570, Adams, Paul D., University of California, Berkeley, CA 94720, Eisenberg, David S., University of California, Los Angeles, CA 90095-1570, University of California, Los Angeles, CA 90095-1570, and Sauter, Nicholas K., E-mail: nksauter@lbl.gov. Sun . "Indexing amyloid peptide diffraction from serial femtosecond crystallography: new algorithms for sparse patterns". Denmark. doi:10.1107/S1399004714026145.
@article{osti_22347713,
title = {Indexing amyloid peptide diffraction from serial femtosecond crystallography: new algorithms for sparse patterns},
author = {Brewster, Aaron S. and Sawaya, Michael R. and University of California, Los Angeles, CA 90095-1570 and University of California, Los Angeles, CA 90095-1570 and Rodriguez, Jose and University of California, Los Angeles, CA 90095-1570 and Hattne, Johan and Echols, Nathaniel and McFarlane, Heather T. and University of California, Los Angeles, CA 90095-1570 and Cascio, Duilio and University of California, Los Angeles, CA 90095-1570 and University of California, Los Angeles, CA 90095-1570 and Adams, Paul D. and University of California, Berkeley, CA 94720 and Eisenberg, David S. and University of California, Los Angeles, CA 90095-1570 and University of California, Los Angeles, CA 90095-1570 and Sauter, Nicholas K., E-mail: nksauter@lbl.gov},
abstractNote = {Special methods are required to interpret sparse diffraction patterns collected from peptide crystals at X-ray free-electron lasers. Bragg spots can be indexed from composite-image powder rings, with crystal orientations then deduced from a very limited number of spot positions. Still diffraction patterns from peptide nanocrystals with small unit cells are challenging to index using conventional methods owing to the limited number of spots and the lack of crystal orientation information for individual images. New indexing algorithms have been developed as part of the Computational Crystallography Toolbox (cctbx) to overcome these challenges. Accurate unit-cell information derived from an aggregate data set from thousands of diffraction patterns can be used to determine a crystal orientation matrix for individual images with as few as five reflections. These algorithms are potentially applicable not only to amyloid peptides but also to any set of diffraction patterns with sparse properties, such as low-resolution virus structures or high-throughput screening of still images captured by raster-scanning at synchrotron sources. As a proof of concept for this technique, successful integration of X-ray free-electron laser (XFEL) data to 2.5 Å resolution for the amyloid segment GNNQQNY from the Sup35 yeast prion is presented.},
doi = {10.1107/S1399004714026145},
journal = {Acta Crystallographica. Section D: Biological Crystallography},
number = Pt 2,
volume = 71,
place = {Denmark},
year = {Sun Feb 01 00:00:00 EST 2015},
month = {Sun Feb 01 00:00:00 EST 2015}
}