Checking nucleic acid crystal structures

The program SFCHECK [Vaguine et al. (1999), Acta Cryst. D55, 191-205] is us ed to survey the quality of the structure-factor data and the agreement of those data with the atomic coordinates in 105 nucleic acid crystal structur es for which structure-factor amplitudes have been deposited in the Nucleic Acid Database [NDB; Berman et al. (1992), Biophys. J. 63, 751-759]. Nuclei c acid structures present a particular challenge for structure-quality eval uations. The majority of these structures, and DNA molecules in particular, have been solved by molecular replacement of the double-helical motif, who se high degree of symmetry can lead to problems in positioning the molecule in the unit cell. In this paper, the overall quality of each structure was evaluated using parameters such as the R factor, the correlation coefficie nt and various atomic error estimates. In addition, each structure is chara cterized by the average values of several local quality indicators, which i nclude the atomic displacement, the density correlation, the B factor and t he density index. The latter parameter measures the relative electron-densi ty level at the atomic position. In order to assess the quality of the mode l in specific regions, the same local quality indicators are also surveyed for individual groups of atoms in each structure. Several of the global qua lity indicators are found to vary linearly with resolution and less than a dozen structures are found to exhibit values significantly different from t he mean for these indicators, showing that the quality of the nucleic acid structures tends to be rather uniform. Analysis of the mutual dependence of the values of different local quality indicators, computed for individual residues and atom groups, reveals that these indicators essentially complem ent each other and are not redundant with the B factor. Using several of th ese indicators, it was found that the atomic coordinates of the nucleic aci d bases tend to be better defined than those of the backbone. One of the lo cal indicators, the density index, is particularly useful in spotting regio ns of the model that rt poorly in the electron density. Using this paramete r, the quality of crystallographic water positions in the analyzed structur es was surveyed and it was found that a sizable fraction of these positions have poorly defined electron density and may therefore not be reliable. Th e possibility that cases of poorly positioned water molecules are symptomat ic of more widespread problems with the structure as a whole is also raised .