Accounting for nonuniformity of bulk‐solvent: A mosaic model

Afonine, Pavel V.; Adams, Paul D.; Sobolev, Oleg V.; Urzhumtsev, Alexandre G.

doi:10.1002/pro.4909

Title: Accounting for nonuniformity of bulk‐solvent: A mosaic model

Journal Article · 14 February 2024 · Protein Science

DOI: https://doi.org/10.1002/pro.4909 · OSTI ID:2305566

^[1]; Adams, Paul D. ^[2]; Sobolev, Oleg V. ^[1]; Urzhumtsev, Alexandre G. ^[3]

Molecular Biophysics &, Integrated Bioimaging Division Lawrence Berkeley National Laboratory Berkeley California USA
Molecular Biophysics &, Integrated Bioimaging Division Lawrence Berkeley National Laboratory Berkeley California USA, Department of Bioengineering University of California Berkeley Berkeley California USA
Centre for Integrative Biology Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS–INSERM‐UdS Illkirch France, Université de Lorraine, Faculté des Sciences et Technologies Vandoeuvre‐les‐Nancy France

Abstract A flat mask‐based model is almost universally used in macromolecular crystallography to account for disordered (bulk) solvent. This model assumes any voxel of the crystal unit cell that is not occupied by the atomic model is occupied by the solvent. The properties of this solvent are assumed to be exactly the same across the whole volume of the unit cell. While this is a reasonable approximation in practice, there are a number of scenarios where this model becomes suboptimal. In this work, we enumerate several of these scenarios and describe a new generalized approach to modeling the bulk‐solvent which we refer to as mosaic bulk‐solvent model. The mosaic bulk‐solvent model allows nonuniform features of the solvent in the crystal to be accounted for in a computationally efficient way. It is implemented in the computational crystallography toolbox and the Phenix software.

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Sponsoring Organization:: USDOE

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 2305566

Journal Information:: Protein Science, Journal Name: Protein Science Journal Issue: 3 Vol. 33; ISSN 0961-8368

Publisher:: Wiley Blackwell (John Wiley & Sons)Copyright Statement

Country of Publication:: United Kingdom

Language:: English

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