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

Abstract

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];  [2];  [1];  [1];  [2];  [2];  [3];  [2];  [1]
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Biosciences Division.
  2. Univ. of California, Los Angeles, CA (United States)
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Los Angeles, CA (United States)
Publication Date:
Research Org.:
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1190539
Grant/Contract Number:  
AC02-05CH11231; FC02-02ER63421
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: 2; 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; XFEL; Sup35 yeast prion; indexing methods; crystallography

Citation Formats

Brewster, Aaron S., Sawaya, Michael R., Rodriguez, Jose, Hattne, Johan, Echols, Nathaniel, McFarlane, Heather T., Cascio, Duilio, Adams, Paul D., Eisenberg, David S., and Sauter, Nicholas K. Indexing amyloid peptide diffraction from serial femtosecond crystallography: New algorithms for sparse patterns. United States: N. p., 2015. Web. doi:10.1107/S1399004714026145.
Brewster, Aaron S., Sawaya, Michael R., Rodriguez, Jose, Hattne, Johan, Echols, Nathaniel, McFarlane, Heather T., Cascio, Duilio, Adams, Paul D., Eisenberg, David S., & Sauter, Nicholas K. Indexing amyloid peptide diffraction from serial femtosecond crystallography: New algorithms for sparse patterns. United States. doi:10.1107/S1399004714026145.
Brewster, Aaron S., Sawaya, Michael R., Rodriguez, Jose, Hattne, Johan, Echols, Nathaniel, McFarlane, Heather T., Cascio, Duilio, Adams, Paul D., Eisenberg, David S., and Sauter, Nicholas K. Fri . "Indexing amyloid peptide diffraction from serial femtosecond crystallography: New algorithms for sparse patterns". United States. doi:10.1107/S1399004714026145. https://www.osti.gov/servlets/purl/1190539.
@article{osti_1190539,
title = {Indexing amyloid peptide diffraction from serial femtosecond crystallography: New algorithms for sparse patterns},
author = {Brewster, Aaron S. and Sawaya, Michael R. and Rodriguez, Jose and Hattne, Johan and Echols, Nathaniel and McFarlane, Heather T. and Cascio, Duilio and Adams, Paul D. and Eisenberg, David S. and Sauter, Nicholas K.},
abstractNote = {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 theComputational 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 (Online)},
number = 2,
volume = 71,
place = {United States},
year = {2015},
month = {1}
}

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