Structural refinement of the DNA-containing capsid of canine parvovirus using RSRef, a resolution-dependent stereochemically restrained real-space refinement method

The canine parvovirus structure (CPV) [Tsao, Chapman, Agbandje, Keller, Smith, Wu, Luo, Smith, Rossmann, Compans & Parrish (1991). Science, 251, 1456-1464] has been refined by a real-space refinement procedure [Chapman (1994). Acta Cryst. A51, 69-80]. The fit of an atomic model to electron density was optimized while taking into account the resolution limit of the data and the stereochemistry of the structure. The refined model had a reasonable free R factor [Brunger (1992). Nature (London), 355, 472-475] of 0.29. The method is particularly fast and convenient when only a small fraction of the crystallographic asymmetric unit needs to be refined, as is the case when there is high noncrystallographic redundancy. Cycles of refinement for virus capsids were completed in about 1/50th of the time required for equivalent reciprocal-space procedures.