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On the distribution of the bulk-solvent correction parameters.
1IMBB, FORTH, PO Box 1527, 71110 Heraklion, Crete, Greece.
Acta Crystallographica. Section D, Biological Crystallography
|August 16, 2000
Summary
Bulk-solvent correction parameters (B(sol), k(sol)) show a wider range and lack of correlation with physical meaning in protein crystal structures. Current algorithms struggle to separate these parameters during macromolecular refinement.
Area of Science:
- Structural Biology
- Crystallography
- Biophysics
Background:
- Macromolecular refinement relies on bulk-solvent correction parameters (B(sol), k(sol)) to model solvent and B-factors.
- These parameters are typically assumed to have specific physical meanings and fall within a narrow range.
Purpose of the Study:
- To analyze the distribution of bulk-solvent correction parameters (B(sol), k(sol)) from a dataset of 219 Protein Data Bank crystal structures.
- To evaluate the observed range, physical interpretation, and interdependence of these parameters.
Main Methods:
- Utilized an exponential scaling algorithm based on Babinet's principle to determine B(sol) and k(sol) values.
- Analyzed the distribution of these parameters across 219 deposited crystal structures.
Main Results:
- Observed parameter ranges for B(sol) and k(sol) are significantly wider than commonly cited values.
- The determined k(sol) values do not consistently correlate with their expected physical interpretations.
- B(sol) and k(sol) are not independent, and a simple exponential function can achieve reasonable agreement with experimental data.
Conclusions:
- Current algorithms used in macromolecular refinement are insufficient to independently determine B(sol) and k(sol).
- The findings suggest a need for re-evaluation of bulk-solvent correction parameterization in crystallographic refinement.