Journal article
A smooth and differentiable bulk-solvent model for macromolecular diffraction
Acta crystallographica. Section D, Biological crystallography., Vol.66(Pt 9), pp.1024-1031
09/01/2010
DOI: 10.1107/S0907444910031045
PMCID: PMC2935282
PMID: 20823553
Abstract
A new method for modeling the bulk solvent in macromolecular diffraction data based on Babinet’s principle is presented. The proposed models offer the advantage of differentiability with respect to atomic coordinates.
Inclusion of low-resolution data in macromolecular crystallography requires a model for the bulk solvent. Previous methods have used a binary mask to accomplish this, which has proven to be very effective, but the mask is discontinuous at the solute–solvent boundary (
i.e.
the mask value jumps from zero to one) and is not differentiable with respect to atomic parameters. Here, two algorithms are introduced for computing bulk-solvent models using either a polynomial switch or a smoothly thresholded product of Gaussians, and both models are shown to be efficient and differentiable with respect to atomic coordinates. These alternative bulk-solvent models offer algorithmic improvements, while showing similar agreement of the model with the observed amplitudes relative to the binary model as monitored using
R
,
R
free
and differences between experimental and model phases. As with the standard solvent models, the alternative models improve the agreement primarily with lower resolution (>6 Å) data
versus
no bulk solvent. The models are easily implemented into crystallographic software packages and can be used as a general method for bulk-solvent correction in macromolecular crystallography.
Details
- Title: Subtitle
- A smooth and differentiable bulk-solvent model for macromolecular diffraction
- Creators
- T. D Fenn - Department of Molecular and Cellular Physiology and Howard Hughes Medical Institute, Stanford, CaliforniaM. J Schnieders - Department of Chemistry, Stanford, CaliforniaA. T Brunger - Department of Molecular and Cellular Physiology and Howard Hughes Medical Institute, Stanford, California
- Resource Type
- Journal article
- Publication Details
- Acta crystallographica. Section D, Biological crystallography., Vol.66(Pt 9), pp.1024-1031
- DOI
- 10.1107/S0907444910031045
- PMID
- 20823553
- PMCID
- PMC2935282
- NLM abbreviation
- Acta Crystallogr D Biol Crystallogr
- ISSN
- 0907-4449
- eISSN
- 1399-0047
- Publisher
- International Union of Crystallography
- Alternative title
- A smooth bulk-solvent model
- Language
- English
- Date published
- 09/01/2010
- Academic Unit
- Roy J. Carver Department of Biomedical Engineering; Biochemistry and Molecular Biology
- Record Identifier
- 9984025267902771
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