The structure determination of a common cold virus, human rhinovirus 14

The methods used to solve the structure of human rhinovirus 14 at 3.0 Å resolution are described in detail. The crystals are cubic, space group P2₁3, a = 445.1 Å with 20-fold non-crystallographic redundancy and with approximately 55% solvent and RNA content. The data used to solve the structure were collected at the Cornell High Energy Synchrotron Source (CHESS) using oscillation photography. Most of the computations were performed on Purdue University's Cyber 205 supercomputer. Two heavy-atom derivative data sets from crystals soaked in 1 and 5 mM KAu(CN)₂ were used to provide isomorphous phasing to 4 Å resolution, although it was subsequently shown that phases beyond 5 Å resolution were random. The phases were refined at 5 Å resolution by five cycles of real-space molecular replacement. Phase extension from 5 to 3 Å was then performed using 60 cycles of real-space molecular replacement while extending the resolution in steps of three reciprocal-lattice points at a time once every three cycles. The 3.5 Å skew-averaged map was easily interpreted and showed 811 of the 855 amino acids in the four distinct viral polypeptide chains. A complete atomic model has been built using FRODO on an Evans & Sutherland PS300 graphics system with respect to the 3.08 Å resolution electron density map. The roles of the non-crystallographic symmetry, solvent content, errors in amplitudes, orientation and translation in the molecular replacement process are discussed.