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Application of profile fitting method to neutron time-of-flight protein single crystal diffraction data collected at the iBIX
We developed and employed a profile fitting method for the peak integration of neutron time-of-flight diffraction data collected by the IBARAKI Biological Crystal Diffractometer (iBIX) at the Japan Proton Accelerator Research Complex (J-PARC) for protein ribonuclease A and α-thrombin single crystals...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5131355/ https://www.ncbi.nlm.nih.gov/pubmed/27905404 http://dx.doi.org/10.1038/srep36628 |
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author | Yano, Naomine Yamada, Taro Hosoya, Takaaki Ohhara, Takashi Tanaka, Ichiro Kusaka, Katsuhiro |
author_facet | Yano, Naomine Yamada, Taro Hosoya, Takaaki Ohhara, Takashi Tanaka, Ichiro Kusaka, Katsuhiro |
author_sort | Yano, Naomine |
collection | PubMed |
description | We developed and employed a profile fitting method for the peak integration of neutron time-of-flight diffraction data collected by the IBARAKI Biological Crystal Diffractometer (iBIX) at the Japan Proton Accelerator Research Complex (J-PARC) for protein ribonuclease A and α-thrombin single crystals. In order to determine proper fitting functions, four asymmetric functions were evaluated using strong intensity peaks. A Gaussian convolved with two back-to-back exponentials was selected as the most suitable fitting function, and a profile fitting algorithm for the integration method was developed. The intensity and structure refinement data statistics of the profile fitting method were compared to those of the summation integration method. It was clearly demonstrated that the profile fitting method provides more accurate integrated intensities and model structures than the summation integration method at higher resolution shells. The integration component with the profile fitting method has already been implemented in the iBIX data processing software STARGazer and its user manual has been prepared. |
format | Online Article Text |
id | pubmed-5131355 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Nature Publishing Group |
record_format | MEDLINE/PubMed |
spelling | pubmed-51313552016-12-15 Application of profile fitting method to neutron time-of-flight protein single crystal diffraction data collected at the iBIX Yano, Naomine Yamada, Taro Hosoya, Takaaki Ohhara, Takashi Tanaka, Ichiro Kusaka, Katsuhiro Sci Rep Article We developed and employed a profile fitting method for the peak integration of neutron time-of-flight diffraction data collected by the IBARAKI Biological Crystal Diffractometer (iBIX) at the Japan Proton Accelerator Research Complex (J-PARC) for protein ribonuclease A and α-thrombin single crystals. In order to determine proper fitting functions, four asymmetric functions were evaluated using strong intensity peaks. A Gaussian convolved with two back-to-back exponentials was selected as the most suitable fitting function, and a profile fitting algorithm for the integration method was developed. The intensity and structure refinement data statistics of the profile fitting method were compared to those of the summation integration method. It was clearly demonstrated that the profile fitting method provides more accurate integrated intensities and model structures than the summation integration method at higher resolution shells. The integration component with the profile fitting method has already been implemented in the iBIX data processing software STARGazer and its user manual has been prepared. Nature Publishing Group 2016-12-01 /pmc/articles/PMC5131355/ /pubmed/27905404 http://dx.doi.org/10.1038/srep36628 Text en Copyright © 2016, The Author(s) http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ |
spellingShingle | Article Yano, Naomine Yamada, Taro Hosoya, Takaaki Ohhara, Takashi Tanaka, Ichiro Kusaka, Katsuhiro Application of profile fitting method to neutron time-of-flight protein single crystal diffraction data collected at the iBIX |
title | Application of profile fitting method to neutron time-of-flight protein single crystal diffraction data collected at the iBIX |
title_full | Application of profile fitting method to neutron time-of-flight protein single crystal diffraction data collected at the iBIX |
title_fullStr | Application of profile fitting method to neutron time-of-flight protein single crystal diffraction data collected at the iBIX |
title_full_unstemmed | Application of profile fitting method to neutron time-of-flight protein single crystal diffraction data collected at the iBIX |
title_short | Application of profile fitting method to neutron time-of-flight protein single crystal diffraction data collected at the iBIX |
title_sort | application of profile fitting method to neutron time-of-flight protein single crystal diffraction data collected at the ibix |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5131355/ https://www.ncbi.nlm.nih.gov/pubmed/27905404 http://dx.doi.org/10.1038/srep36628 |
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