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Title: Evaluation of models determined by neutron diffraction and proposed improvements to their validation and deposition

The Protein Data Bank (PDB) contains a growing number of models that have been determined using neutron diffraction or a hybrid method that combines X-ray and neutron diffraction. The advantage of neutron diffraction experiments is that the positions of all atoms can be determined, including H atoms, which are hardly detectable by X-ray diffraction. This allows the determination of protonation states and the assignment of H atoms to water molecules. Because neutrons are scattered differently by hydrogen and its isotope deuterium, neutron diffraction in combination with H/D exchange can provide information on accessibility, dynamics and chemical lability. In this study, the deposited data, models and model-to-data fit for all PDB entries that used neutron diffraction as the source of experimental data have been analysed. In many cases, the reported R work and R free values were not reproducible. In such cases, the model and data files were analysed to identify the reasons for this mismatch. The issues responsible for the discrepancies are summarized and explained. The analysis unveiled limitations to the annotation, deposition and validation of models and data, and a lack of community-wide accepted standards for the description of neutron models and data, as well as deficiencies in currentmore » model refinement tools. Most of the issues identified concern the handling of H atoms. Since the primary use of neutron macromolecular crystallography is to locate and directly visualize H atoms, it is important to address these issues, so that the deposited neutron models allow the retrieval of the maximum amount of information with the smallest effort of manual intervention. A path forward to improving the annotation, validation and deposition of neutron models and hybrid X-ray and neutron models is suggested.« less
Authors:
 [1] ; ORCiD logo [2] ; ORCiD logo [1] ;  [3] ;  [4]
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Shanghai Univ., Shanghai (People's Republic of China)
  3. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  4. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)
Publication Date:
Grant/Contract Number:
AC02-05CH11231; AC03-76SF00098
Type:
Published Article
Journal Name:
Acta Crystallographica. Section D. Structural Biology
Additional Journal Information:
Journal Volume: 74; Journal Issue: 8; Journal ID: ISSN 2059-7983
Publisher:
IUCr
Research Org:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; model validation; neutron crystallography; PDB data mining; H/D exchange; Phenix
OSTI Identifier:
1461576
Alternate Identifier(s):
OSTI ID: 1477262

Liebschner, Dorothee, Afonine, Pavel V., Moriarty, Nigel W., Langan, Paul, and Adams, Paul D.. Evaluation of models determined by neutron diffraction and proposed improvements to their validation and deposition. United States: N. p., Web. doi:10.1107/S2059798318004588.
Liebschner, Dorothee, Afonine, Pavel V., Moriarty, Nigel W., Langan, Paul, & Adams, Paul D.. Evaluation of models determined by neutron diffraction and proposed improvements to their validation and deposition. United States. doi:10.1107/S2059798318004588.
Liebschner, Dorothee, Afonine, Pavel V., Moriarty, Nigel W., Langan, Paul, and Adams, Paul D.. 2018. "Evaluation of models determined by neutron diffraction and proposed improvements to their validation and deposition". United States. doi:10.1107/S2059798318004588.
@article{osti_1461576,
title = {Evaluation of models determined by neutron diffraction and proposed improvements to their validation and deposition},
author = {Liebschner, Dorothee and Afonine, Pavel V. and Moriarty, Nigel W. and Langan, Paul and Adams, Paul D.},
abstractNote = {The Protein Data Bank (PDB) contains a growing number of models that have been determined using neutron diffraction or a hybrid method that combines X-ray and neutron diffraction. The advantage of neutron diffraction experiments is that the positions of all atoms can be determined, including H atoms, which are hardly detectable by X-ray diffraction. This allows the determination of protonation states and the assignment of H atoms to water molecules. Because neutrons are scattered differently by hydrogen and its isotope deuterium, neutron diffraction in combination with H/D exchange can provide information on accessibility, dynamics and chemical lability. In this study, the deposited data, models and model-to-data fit for all PDB entries that used neutron diffraction as the source of experimental data have been analysed. In many cases, the reported R work and R free values were not reproducible. In such cases, the model and data files were analysed to identify the reasons for this mismatch. The issues responsible for the discrepancies are summarized and explained. The analysis unveiled limitations to the annotation, deposition and validation of models and data, and a lack of community-wide accepted standards for the description of neutron models and data, as well as deficiencies in current model refinement tools. Most of the issues identified concern the handling of H atoms. Since the primary use of neutron macromolecular crystallography is to locate and directly visualize H atoms, it is important to address these issues, so that the deposited neutron models allow the retrieval of the maximum amount of information with the smallest effort of manual intervention. A path forward to improving the annotation, validation and deposition of neutron models and hybrid X-ray and neutron models is suggested.},
doi = {10.1107/S2059798318004588},
journal = {Acta Crystallographica. Section D. Structural Biology},
number = 8,
volume = 74,
place = {United States},
year = {2018},
month = {7}
}

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Crystal structure refinement with SHELXL
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PHENIX: a comprehensive Python-based system for macromolecular structure solution
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