Summary information and primary citation
- PDB-id
-
1rmv;
DSSR-derived features in text and
JSON formats; DNAproDB
- Class
- virus-RNA
- Method
- fiber diffraction
- Summary
- Ribgrass mosaic virus, fiber diffraction
- Reference
-
Wang H, Stubbs G (1993): "Molecular
dynamics in refinement against fiber diffraction
data." Acta Crystallogr.,Sect.A,
49, 504-513. doi: 10.1107/S0108767392011255.
- Abstract
- 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.
