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

Journal Article · Tue Jul 24 00:00:00 EDT 2018 · Acta Crystallographica. Section D. Structural Biology

DOI:https://doi.org/10.1107/S2059798318004588· OSTI ID:1461576

Liebschner, Dorothee; Afonine, Pavel V. ; Moriarty, Nigel W. ; Langan, Paul; Adams, Paul D.

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.

• Research Organization: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
• Sponsoring Organization: USDOE Office of Science (SC)
• Grant/Contract Number: AC03-76SF00098; AC02-05CH11231
• OSTI ID: 1461576
• Alternate ID(s): OSTI ID: 1477262
• Journal Information: Acta Crystallographica. Section D. Structural Biology, Journal Name: Acta Crystallographica. Section D. Structural Biology Vol. 74 Journal Issue: 8; ISSN 2059-7983
• Publisher: International Union of Crystallography (IUCr)
• Country of Publication: United Kingdom
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
model validation
neutron crystallography
PDB data mining
H/D exchange
Phenix