Section 21.2.3.1.3.2. Assessing the quality in specific regions of a model

The main purpose for computing the four local quality measures, the B factor, the Density index, the atomic displacement (Shift) and the Density correlation (Table 21.2.3.3), is to identify problem regions in a model. In order to do this effectively, it is necessary to evaluate the degree of redundancy between these measures and to establish the standard ranges for their values. The latter task, in particular, is not straightforward since it depends crucially on the quality of the experimental data and biases introduced by the scaling procedure and refinement protocol. In this regard, several issues are presently still under investigation.

A preliminary investigation of the mutual relations between the above-mentioned local measures has been performed in several protein and nucleic acid structures taken individually. This shows that that the B factor is strongly correlated with the density index, as illustrated in Fig. 21.2.3.5(a), and to a lesser extent with the atomic displacement (Fig. 21.2.3.5b). A weaker correlation was detected between the latter three measures and the residue density correlation (data not shown).

Figure 21.2.3.5| top | pdf | Pairwise correlations between the various local quality indicators computed by SFCHECK. (a) Correlation between the average residue B factor and the density index, and (b) between the B factor and the atomic displacement. The values displayed were computed for residues in the crystal structure of carboxypeptidase (1YME). The meaning of the parameters displayed is given in Table 21.2.3.3.

Analyses across structures could, in principle, be carried out for all four local measures computed by SFCHECK, provided these measures are not subject to systematic biases due to differences in scaling procedures and refinement practices. Such biases are, however, well known for the B factors of individual atoms or residues. This is illustrated in Fig. 21.2.3.6(a). This figure plots, side-by-side, the average residue B factors in 21 protein structures determined at different d spacings. It shows that for proteins determined at poorer resolution (d spacing above 2 Å), the B factors of different structures are systematically shifted relative to one another. Such systematic shifts are much smaller for structures determined at 2 Å resolution or better (Fig. 21.2.3.6a). This is not surprising, since in lower-resolution structures, is often too low (< 4) to yield meaningful values for the B factors.

Figure 21.2.3.6| top | pdf | B factors and density indices for residues across different structures. (a) Average B values in residues of 21 protein structures; (b) average density indices of the same set of residues and structures. The 21 protein structures analysed are from the following PDB entries: 1YME, 1MCT, 1PDO, 1VHH, 1WBA, 1CNS, 1RG7, 1UCO, 1BRO, 1EMB, 1FXI, 1KBA, 1XSM, 1HIB, 1IVF, 1QRS, 1AGX, 1NSN, 1ZOO, 1TGK, 1JCK.

Interestingly, the residue Density index, a very different parameter from the B factor, which measures the level of electron density at the atomic positions, does not display the systematic shifts observed for the B factors (Fig. 21.2.3.6b), despite the fact that the two measures are rather strongly correlated in individual structures. An indicator such as this one, and ultimately the atomic s.u.'s themselves, should be better suited for analysing and comparing the trends in the quality of specific regions of the model across different structures.