Phase refinement virus crystals

Phase information was obtained by combining an X-ray structure of the major capsid protein with a cryo-EM reconstruction of the virus. The position and orientation of this model were refined against the experimental data, separately for the two crystal forms, using XPLOR3.1 (Brunger, 1992). An initial estimate of the particle orientation was obtained from a self-rotation fimction. Patterson correlation refinement was performed against 60-15 A resolution data to optimize the orientation. The position and orientation of the particle were then... 

There are six subunits in the asymmetric unit of the Panuliris structure, arranged in a particle best described as a trimer of dimers. The 3-2 symmetry was good enough to be useful in a phase extension technique commonly used in the structure determination of highly symmetric viruses. Unfortunately, these crystals diffract only to 3.2 A, so that there cannot be a high level of detail available for description of the active site. Nevertheless, because there are six independent copies of the molecule in the asymmetric unit, there is more information than might normally be available at this resolution. The structure has been carefully refined at this resolution, with and without the 3-2 symmetry restraint. The estimated coordinate error is —0.35 A. The overall R is 0.201 for data between 8 and 3.2 A. Surprisingly, while the overalls for subunits 1 and... 

X-ray and neutron diffraction patterns can be detected when a wave is scattered by a periodic structure of atoms in an ordered array such as a crystal or a fiber. The diffraction patterns can be interpreted directly to give information about the size of the unit cell, information about the symmetry of the molecule, and, in the case of fibers, information about periodicity. The determination of the complete structure of a molecule requires the phase information as well as the intensity and frequency information. The phase can be determined using the method of multiple isomor-phous replacement where heavy metals or groups containing heavy element are incorporated into the diffracting crystals. The final coordinates of biomacromolecules are then deduced using knowledge about the primary structure and are refined by processes that include comparisons of calculated and observed diffraction patterns. Three-dimensional structures of proteins and their complexes (Blundell and Johnson, 1976), nucleic acids, and viruses have been determined by X-ray and neutron diffractions. 

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