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

ABSTRACT: 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 Rwork and Rfree 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.

SUBMITTER: Liebschner D

PROVIDER: S-EPMC6079631 | biostudies-literature | 2018 Aug

REPOSITORIES: biostudies-literature

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

Liebschner Dorothee D Afonine Pavel V PV Moriarty Nigel W NW Langan Paul P Adams Paul D PD

Acta crystallographica. Section D, Structural biology 20180724 Pt 8

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 ...[more]

PMID: 30082516

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Project description:We report high-pressure neutron powder diffraction measurements of the most hydrated phase in the MgSO4–H2O system, magnesium sulfate undecahydrate, including an analysis of the elastic strain tensor and observations concerning phase changes that occur at high pressure. We have collected neutron powder diffraction data from MgSO4·11D2O (the deuterated analogue of meridianiite), a highly hydrated sulfate salt that is thought to be a candidate rock-forming mineral in some icy satellites of the outer solar system. Our measurements, made using the PEARL/HiPr and OSIRIS instruments at the ISIS neutron spallation source, covered the range 0.1 < P < 800?MPa and 150 < T < 280?K. The refined unit-cell volumes as a function of P and T are parameterized in the form of a Murnaghan integrated linear equation of state having a zero-pressure volume V0 = 706.23?(8)?Å3, zero-pressure bulk modulus K0 = 19.9?(4)?GPa and its first pressure derivative, K? = 9?(1). The structure’s compressibility is highly anisotropic, as expected, with the three principal directions of the unit-strain tensor having compressibilities of 9.6?×?10?3, 3.4?×?10?2 and 3.4?×?10?3 GPa?1, the most compressible direction being perpendicular to the long axis of a discrete hexadecameric water cluster, (D2O)16. At high pressure we observed two different phase transitions. First, warming of MgSO4·11D2O at 545?MPa resulted in a change in the diffraction pattern at 275?K consistent with partial (peritectic) melting; quasielastic neutron spectra collected simultaneously evince the onset of the reorientational motion of D2O molecules with characteristic time-scales of 20–30?ps, longer than those found in bulk liquid water at the same temperature and commensurate with the lifetime of solvent-separated ion pairs in aqueous MgSO4. Second, at ??0.9?GPa, 240?K, MgSO4·11D2O decomposed into high-pressure water ice phase VI and MgSO4·9D2O, a recently discovered phase that has hitherto only been formed at ambient pressure by quenching small droplets of MgSO4(aq) in liquid nitrogen. The fate of the high-pressure enneahydrate on further compression and warming is not clear from the neutron diffraction data, but its occurrence indicates that it may also be a rock-forming mineral in the deep mantles of large icy satellites.

Dataset Information

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

Publications

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

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