What are the current limits on determination of protonation state using neutron macromolecular crystallography?

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

doi:10.1016/bs.mie.2020.01.008

Title: What are the current limits on determination of protonation state using neutron macromolecular crystallography?

Book · Thu Feb 13 00:00:00 EST 2020 · Methods in Enzymology

DOI:https://doi.org/10.1016/bs.mie.2020.01.008· OSTI ID:1983881

Liebschner, Dorothee ^[1]; Afonine, Pavel V. ^[1]; Moriarty, Nigel W. ^[1]; Adams, Paul D. ^[2]

Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); University of California Berkeley, CA (United States)

The rate of deposition of models determined by neutron diffraction, or a hybrid approach that combines X-ray and neutron diffraction, has increased in recent years. The benefit of neutron diffraction is that hydrogen atom (H) positions are detectable, allowing for the determination of protonation state and water molecule orientation. This study analyses all neutron models deposited in the Protein Data Bank to date, focusing on protonation state and properties of H (or deuterium, D) atoms as well as the details of water molecules. In particular, clashes and hydrogen bonds involving H or D atoms are investigated. As water molecules are typically the least reproducible part of a structural model, their positions in neutron models were compared to those in homologous high-resolution X-ray structures. For models determined by joint refinement against X-ray and neutron data, the water structure comparison was also carried out for models re-refined against the X-ray data alone. The homologues have generally fewer conserved water molecules where X-ray only was used and the positions of equivalent waters vary more than in the case of the hybrid X-ray model. As neutron diffraction data are generally less complete than X-ray data, the influence of neutron data completeness on nuclear density maps was also analyzed. Here, we observe and discuss systematic map quality deterioration as result of data incompleteness.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); US National Institutes of Health (NIH)

DOE Contract Number:: AC02-05CH11231; P01GM063210; R01GM071939

OSTI ID:: 1983881

Journal Information:: Methods in Enzymology, Vol. 634; Related Information: Book Title: Neutron Crystallography in Structural Biology; ISSN 0076-6879

Publisher:: Elsevier

Country of Publication:: United States

Language:: English

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Title: What are the current limits on determination of protonation state using neutron macromolecular crystallography?

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