International
Tables for Crystallography Volume F Crystallography of biological macromolecules Edited by M. G. Rossmann and E. Arnold © International Union of Crystallography 2006 |
International Tables for Crystallography (2006). Vol. F. ch. 18.2, p. 376
Figure 18.2.2.1
a
The Howard Hughes Medical Institute, and Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, and Stanford Synchrotron Radiation Laboratory, Stanford Universty, 1201 Welch Road, MSLS P210, Stanford, CA 94305-5489, USA,bThe Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA, and cDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA |
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Figure 18.2.2.1
Effect of resolution on coordinate-error estimates: accuracy as a function of resolution. Refinements were begun with the crystal structure of penicillopepsin (Hsu et al., 1977) with water molecules omitted and with uniform temperature factors. The low-resolution limit was set to 6 Å. Inclusion of all low-resolution diffraction data does not change the conclusions (Adams et al., 1997). The penicillopepsin diffraction data were artificially truncated to the specified high-resolution limit. Each refinement consisted of simulated annealing using a Cartesian-space slow-cooling protocol starting at 2000 K, overall B-factor refinement and individual restrained B-factor refinement. All refinements were carried out with 10% of the diffraction data randomly omitted for cross validation. (a) Coordinate-error estimates of the refined structures using the methods of Luzzati (1952) and Read (1986). All observed diffraction data were used, i.e. no cross validation was performed. The actual coordinate errors (r.m.s. differences to the original crystal structure) are shown for comparison. (b) Cross-validated coordinate-error estimates. The test set was used to compute the coordinate-error estimates (Kleywegt & Brünger, 1996). |