SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model

Abstract

In this paper we present SFCHECK, a stand-alone software package that features a uni®ed set of procedures for evaluating the structure-factor data obtained from X-ray diffraction experiments and for assessing the agreement of the atomic coordinates with these data. The evaluation is performed completely automatically, and produces a concise PostScript pictorial output similar to that of PROCHECK [Laskowski, MacArthur, Moss & Thornton (1993). J. Appl. Cryst. 26, 283±291], greatly facilitating visual inspection of the results. The required inputs are the structure-factor amplitudes and the atomic coordinates. Having those, the program summarizes relevant information on the deposited structure factors and evaluates their quality using criteria such as data completeness, structure-factor uncertainty and the optical resolution computed from the Patterson origin peak. The dependence of various parameters on the nominal resolution (d spacing) is also given. To evaluate the global agreement of the atomic model with the experimental data, the program recomputes the R factor, the correlation coef®cient between observed and calculated structure-factor amplitudes and R free (when appropriate). In addition, it gives several estimates of the average error in the atomic coordinates. The local agreement between the model and the electron-density map is evaluated on a per-residue basis, considering separately the macromolecule backbone and side-chain atoms, as well as solvent atoms and heterogroups. Among the criteria are the normalized average atomic displacement, the local density correlation coef®cient and the polymer chain connectivity. The possibility of computing these criteria using the omit-map procedure is also provided. The described software should be a valuable tool in monitoring the re®nement procedure and in assessing structures deposited in databases.

Probing the Active Center of Benzaldehyde Lyase with Substitutions and the Pseudosubstrate Analogue Benzoylphosphonic Acid Methyl Ester

“…A number of regions were observed to be disordered in the final structure and are indicated in Table 1. The final structural solution was subjected to validation using SFCheck, ProCheck and WhatCheck (27)(28)(29).…”

Crystallization and preliminary X-ray characterization of the nitrile reductase QueF: a queuosine-biosynthesis enzyme

“…Using the coordinates of bound GTP in the GTP-CH-I structure, a 7-cyano-7-deazaguanine molecule was docked onto the putative active site that was located at the intersubunit interface. The final model was energy-minimized in CNS (Brü nger et al, 1998) and validated in PROCHECK (Vaguine et al, 1999). The model had a standard Ramachandran plot with 90.2% of residues falling in favored regions and 8.3 and 1.5% in the allowed and generously allowed regions, respectively.…”

Structural basis for telmisartan-mediated partial activation of PPAR gamma

“…21 The structure of human PPARg LBD was solved by molecular replacement using MOLREP 22,23 against an existing in-house structure of the human PPARg LBD. Crystals belonged to the orthorhombic space group P2 1 2 1 2, with cell axes of a¼132.9 Å , b¼53.5 Å and c¼53.9 Å .…”