Gerald Stubbs
Last active: 2/15/2016

Molecular dynamics in refinement against fiber diffraction data.

Wang H, Stubbs G
Acta Crystallogr A. 1993 49 (3): 504-13

PMID: 8129880 · DOI:10.1107/s0108767392011255

The molecular dynamics (MD) method has been adapted for refinement of the structures of helical macromolecular aggregates aginst X-ray fiber diffraction data. To test the effectiveness of the method, refinements of the tobacco mosaic virus structure were carried out against a set of simulated fiber diffraction intensities using the MD method as well as the conventional restrained least-squares (RLS) method. The MD refinement converged to a very low R factor and produced a structure with generally satisfactory sterochemistry, while the RLS refinemnt was trapped at a local energy minimum with a larger R factor. Results suggest that the effective experimental radius of convergence of the MD method is significantly greater than that of the RLS method. Even when the initial structure is too far from the true structure to allow direct refinement, the MD method is able to find local minima that resemble the true structure sufficiently to allow improved phasing and thus lead to interpretable difference maps for model rebuilding.

MeSH Terms (5)

Capsid Mathematics Software Tobacco Mosaic Virus X-Ray Diffraction

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