Cargando…
Indexing amyloid peptide diffraction from serial femtosecond crystallography: new algorithms for sparse patterns
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 Comput...
Autores principales: | , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
International Union of Crystallography
2015
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4321489/ https://www.ncbi.nlm.nih.gov/pubmed/25664747 http://dx.doi.org/10.1107/S1399004714026145 |
_version_ | 1782356273420828672 |
---|---|
author | 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. |
author_facet | 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. |
author_sort | Brewster, Aaron S. |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-4321489 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | International Union of Crystallography |
record_format | MEDLINE/PubMed |
spelling | pubmed-43214892015-02-20 Indexing amyloid peptide diffraction from serial femtosecond crystallography: new algorithms for sparse patterns 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. Acta Crystallogr D Biol Crystallogr Research Papers 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. International Union of Crystallography 2015-01-23 /pmc/articles/PMC4321489/ /pubmed/25664747 http://dx.doi.org/10.1107/S1399004714026145 Text en © Brewster et al. 2015 http://creativecommons.org/licenses/by/2.0/uk/ 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. |
spellingShingle | Research Papers 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 |
title | Indexing amyloid peptide diffraction from serial femtosecond crystallography: new algorithms for sparse patterns |
title_full | Indexing amyloid peptide diffraction from serial femtosecond crystallography: new algorithms for sparse patterns |
title_fullStr | Indexing amyloid peptide diffraction from serial femtosecond crystallography: new algorithms for sparse patterns |
title_full_unstemmed | Indexing amyloid peptide diffraction from serial femtosecond crystallography: new algorithms for sparse patterns |
title_short | Indexing amyloid peptide diffraction from serial femtosecond crystallography: new algorithms for sparse patterns |
title_sort | indexing amyloid peptide diffraction from serial femtosecond crystallography: new algorithms for sparse patterns |
topic | Research Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4321489/ https://www.ncbi.nlm.nih.gov/pubmed/25664747 http://dx.doi.org/10.1107/S1399004714026145 |
work_keys_str_mv | AT brewsteraarons indexingamyloidpeptidediffractionfromserialfemtosecondcrystallographynewalgorithmsforsparsepatterns AT sawayamichaelr indexingamyloidpeptidediffractionfromserialfemtosecondcrystallographynewalgorithmsforsparsepatterns AT rodriguezjose indexingamyloidpeptidediffractionfromserialfemtosecondcrystallographynewalgorithmsforsparsepatterns AT hattnejohan indexingamyloidpeptidediffractionfromserialfemtosecondcrystallographynewalgorithmsforsparsepatterns AT echolsnathaniel indexingamyloidpeptidediffractionfromserialfemtosecondcrystallographynewalgorithmsforsparsepatterns AT mcfarlaneheathert indexingamyloidpeptidediffractionfromserialfemtosecondcrystallographynewalgorithmsforsparsepatterns AT cascioduilio indexingamyloidpeptidediffractionfromserialfemtosecondcrystallographynewalgorithmsforsparsepatterns AT adamspauld indexingamyloidpeptidediffractionfromserialfemtosecondcrystallographynewalgorithmsforsparsepatterns AT eisenbergdavids indexingamyloidpeptidediffractionfromserialfemtosecondcrystallographynewalgorithmsforsparsepatterns AT sauternicholask indexingamyloidpeptidediffractionfromserialfemtosecondcrystallographynewalgorithmsforsparsepatterns |