Structure Determination of the X174 Closed Procapsid

The structure of a procapsid of the single-stranded DNA bacteriophage φX174 was determined to 3.5 Å resolution. The crystal space group was I2₁3 with a unit-cell length of 774 Å. The unit cell contained 16 icosahedral virus particles, each situated on a crystallographic three-fold axis. Thus, there are two independent one-thirds of a particle per asymmetric unit, and a total of 40-fold non-crystallographic redundancy. To aid in the interpretation of the packing arrangement, crystals were prepared for thin sectioning and analyzed by electron microscopy. Oscillation X-ray diffraction data was collected on image plates using synchrotron radiation and oscillation angles of either 0.25 or 0.30°. A low-resolution 6.5 Å data set collected from a single frozen crystal was particularly helpful in the structure determination, because of its completeness and internal consistency. The initial particle orientations were determined using self-rotation functions, while the initial position of one particle was determined from a Patterson map. The structure was solved by molecular replacement real-space averaging using a model based on a cryo-electron microscopy reconstruction as a starting point for the phase determination. The initial structure determination used the data between 20 and 13 Å resolution, which was then extended one reciprocal lattice point at a time to 6.5 Å resolution. At this point, a 3.5 Å resolution data set compiled from a number of crystals collected at 277 K was introduced. Phase extension and averaging continued to 3.5 Å resolution after re-determining the particle positions and orien­tations. The amino-acid sequences of most of the D, F and G proteins and part of the B protein could be un­ambiguously built into the 3.5 Å electron-density map. Partial crystallographic refinement yielded an R factor of 31.6%, consistent with the relatively low resolution and lack of completeness of the data.