International
Tables for
Crystallography
Volume F
Crystallography of biological macromolecules
Edited by M. G. Rossmann and E. Arnold

International Tables for Crystallography (2006). Vol. F, ch. 21.3, p. 522   | 1 | 2 |

Figure 21.3.5.1 

O. Dym,a D. Eisenbergb* and T. O. Yeatesc

aUCLA–DOE Laboratory of Structural Biology and Molecular Medicine, UCLA, Box 951570, Los Angeles, CA 90095-1570, USA, bUCLA–DOE Laboratory of Structural Biology and Molecular Medicine, Department of Chemistry & Biochemistry, Molecular Biology Institute and Department of Biological Chemistry, UCLA, Los Angeles, CA 90095-1570, USA, and  cUCLA–DOE Laboratory of Structural Biology and Molecular Medicine, Department of Chemistry & Biochemistry and Molecular Biology Institute, UCLA, Los Angeles, CA 90095-1569, USA
Correspondence e-mail:  david@mbi.ucla.edu

[Figure 21.3.5.1]
Figure 21.3.5.1

Detection of errors in the small subunit of ribulose-1,5-bisphospate carboxylase/oxygenase (RuBisCO). (a) ERRAT plot of the error function in a nine-residue sliding window, the centre of which is at the sequence position indicated by the horizontal axis. The solid bold line represents the revised structure and the dashed line the original structure. The thin solid lines indicate the 95% and 99% confidence limits for rejection. A region above the 95% line can be judged incorrect with 95% certainty. (b) VERIFY3D profile-window plots for the revised (bold) and original (dashed) models. The vertical axis gives the average 3D–1D score for residues within a 21-residue sliding window. Regions that score below zero are suspect. (c) Ramachandran diagram from PROCHECK of the initial structure of RuBisCO. The main-chain dihedral angle ϕ (N—Cα bond) is plotted versus ψ (Cα—C bond). All non-glycine residues outside the allowed regions are marked. (d) Ramachandran plot for the refined RuBisCO structure.