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Acta Crystallographica Section D
Protein imperfections: separating intrinsic from extrinsic variation of torsion angles
Glenn L. Butterfoss,a Jane S. Richardsonb and Jan Hermansa* a Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599-7260, USA, and bDepartment of Biochemistry, Duke University Medical School, Durham, North Carolina 27710-3711, USA
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In this paper, the variation of the values of dihedral angles in proteins is divided into two categories by analyzing distributions in a database of structures determined at a resolution of Ê 1.8 A or better [Lovell et al. (2003), Proteins Struct. Funct. Genet. 50, 437±450]. The ®rst analysis uses the torsion angle for the CÐC bond (11) of all Gln, Glu, Arg and Lys residues (`unbranched set'). Plateaued values at low B values imply a root-mean-square deviation (RMSD) of just 9 for 11 related to intrinsic structural differences between proteins. Extrapolation to high resolution gives a value of 11 , while over the entire database the RMSD is 13.4 . The assumption that the deviations arise from independent intrinsic and extrinsic sources gives $10 as the RMSD for 11 of these unbranched side chains arising from all disorder and error over the entire set. It is also found that the decrease in 11 deviation that is correlated with higher resolution structures is almost entirely a consequence of the higher percentage of low-B-value side chains in those structures and furthermore that the crystal temperature at which diffraction data are collected has a negligible effect on intrinsic deviation. Those intrinsic aspects of the distributions not related to statistical or other errors, data incompleteness or disorder correlate with energies of model…...