Structure determination of the φX174 closed procapsid

The structure of a procapsid of the single-stranded DNA bacteriophage phi X174 was determined to 3.5 Angstrom resolution. The crystal space group was I2(1)3 with a unit-cell length of 774 Angstrom. The unit cell contained 16 icosahedral virus particles. each situated on a crystallographic threefold 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 degrees. A low-resolution 6.5 Angstrom 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 Angstrom resolution, which was then extended one reciprocal lattice point at a time to 6.5 A resolution. At this paint. a 3.5 Angstrom resolution data set compiled from a number of crystals collected at 277 K was introduced. Phase extension and averaging continued to 3.5 Angstrom 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 Angstrom 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.