Structure Determination of the X174 Closed Procapsid
Acta Crystallographica Section D
Volume 54, Issue 5, pages 878–890, September 1998
How to Cite
Dokland, T., McKenna, R., Sherman, D. M., Bowman, B. R., Bean, W. F. and Rossmann, M. G. (1998), Structure Determination of the X174 Closed Procapsid. Acta Crystallographica Section D, 54: 878–890. doi: 10.1107/S0907444998002467
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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.