Structure determination of monoclinic canine parvovirus

Abstract

The three-dimensional structure of the single-stranded DNA canine parvovirus has been determined to 3.25 A resolution. Monoclinic crystals belonging to space group P2(1) (a = 263.1, b = 348.9, c = 267.2 A, beta = 90.82 degrees) were selected for data collection using primarily the Cornell High Energy Synchrotron Source and oscillation photography. There was one icosahedral particle per crystallographic asymmetric unit, giving 60-fold redundancy. The particle orientations in the unit cell were determined with a rotation function. The rough positions of the particles in the unit cell were estimated by considering the packing of spheres into the P2(1) crystal cell. More accurate particle centers were determined from Harker peaks in a Patterson function. Hollow-shell models were used to compute phases to 20 A resolution. The radii of the models were based on packing considerations, the fit of spherical shells to the low-resolution X-ray data and low-angle solution scattering data. The phases were extended to 9 A resolution using molecular replacement real-space averaging. These were then used to determine the heavy-atom position of a K2PtBr6 derivative, for which only 5% of the theoretically observable reflections had been recorded. The center of gravity of the 60 independent heavy-atom sites gave an improved particle center position. Single isomorphous replacement phases to 8 A resolution were then calculated with the platinum derivative. These were used to initiate phase improvement and extension to 3.25 A resolution using density averaging and Fourier back-transformation in steps of one reciprocal lattice point at a time. The resulting electron density map was readily interpretable and an atomic model was built into the electron density map on a PS390 graphics system using the FRODO program. The R factor prior to structure refinement for data between 5.0 and 3.25 A was 36%.