Cargando…
Identification of rogue datasets in serial crystallography
Advances in beamline optics, detectors and X-ray sources allow new techniques of crystallographic data collection. In serial crystallography, a large number of partial datasets from crystals of small volume are measured. Merging of datasets from different crystals in order to enhance data completene...
Autores principales: | , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
International Union of Crystallography
2016
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4886987/ https://www.ncbi.nlm.nih.gov/pubmed/27275144 http://dx.doi.org/10.1107/S1600576716005471 |
_version_ | 1782434676147748864 |
---|---|
author | Assmann, Greta Brehm, Wolfgang Diederichs, Kay |
author_facet | Assmann, Greta Brehm, Wolfgang Diederichs, Kay |
author_sort | Assmann, Greta |
collection | PubMed |
description | Advances in beamline optics, detectors and X-ray sources allow new techniques of crystallographic data collection. In serial crystallography, a large number of partial datasets from crystals of small volume are measured. Merging of datasets from different crystals in order to enhance data completeness and accuracy is only valid if the crystals are isomorphous, i.e. sufficiently similar in cell parameters, unit-cell contents and molecular structure. Identification and exclusion of non-isomorphous datasets is therefore indispensable and must be done by means of suitable indicators. To identify rogue datasets, the influence of each dataset on CC(1/2) [Karplus & Diederichs (2012 ▸). Science, 336, 1030–1033], the correlation coefficient between pairs of intensities averaged in two randomly assigned subsets of observations, is evaluated. The presented method employs a precise calculation of CC(1/2) that avoids the random assignment, and instead of using an overall CC(1/2), an average over resolution shells is employed to obtain sensible results. The selection procedure was verified by measuring the correlation of observed (merged) intensities and intensities calculated from a model. It is found that inclusion and merging of non-isomorphous datasets may bias the refined model towards those datasets, and measures to reduce this effect are suggested. |
format | Online Article Text |
id | pubmed-4886987 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | International Union of Crystallography |
record_format | MEDLINE/PubMed |
spelling | pubmed-48869872016-06-06 Identification of rogue datasets in serial crystallography Assmann, Greta Brehm, Wolfgang Diederichs, Kay J Appl Crystallogr Research Papers Advances in beamline optics, detectors and X-ray sources allow new techniques of crystallographic data collection. In serial crystallography, a large number of partial datasets from crystals of small volume are measured. Merging of datasets from different crystals in order to enhance data completeness and accuracy is only valid if the crystals are isomorphous, i.e. sufficiently similar in cell parameters, unit-cell contents and molecular structure. Identification and exclusion of non-isomorphous datasets is therefore indispensable and must be done by means of suitable indicators. To identify rogue datasets, the influence of each dataset on CC(1/2) [Karplus & Diederichs (2012 ▸). Science, 336, 1030–1033], the correlation coefficient between pairs of intensities averaged in two randomly assigned subsets of observations, is evaluated. The presented method employs a precise calculation of CC(1/2) that avoids the random assignment, and instead of using an overall CC(1/2), an average over resolution shells is employed to obtain sensible results. The selection procedure was verified by measuring the correlation of observed (merged) intensities and intensities calculated from a model. It is found that inclusion and merging of non-isomorphous datasets may bias the refined model towards those datasets, and measures to reduce this effect are suggested. International Union of Crystallography 2016-04-18 /pmc/articles/PMC4886987/ /pubmed/27275144 http://dx.doi.org/10.1107/S1600576716005471 Text en © Greta Assmann et al. 2016 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 Assmann, Greta Brehm, Wolfgang Diederichs, Kay Identification of rogue datasets in serial crystallography |
title | Identification of rogue datasets in serial crystallography
|
title_full | Identification of rogue datasets in serial crystallography
|
title_fullStr | Identification of rogue datasets in serial crystallography
|
title_full_unstemmed | Identification of rogue datasets in serial crystallography
|
title_short | Identification of rogue datasets in serial crystallography
|
title_sort | identification of rogue datasets in serial crystallography |
topic | Research Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4886987/ https://www.ncbi.nlm.nih.gov/pubmed/27275144 http://dx.doi.org/10.1107/S1600576716005471 |
work_keys_str_mv | AT assmanngreta identificationofroguedatasetsinserialcrystallography AT brehmwolfgang identificationofroguedatasetsinserialcrystallography AT diederichskay identificationofroguedatasetsinserialcrystallography |