Abstract
The accuracy of B factors in protein crystal structures has been determined by comparing the same atoms in numerous, independent crystal structures of Gallus gallus lysozyme. Both B-factor absolute differences and normal probability plots indicate that the estimated B-factor errors are quite large, close to 9 Å2 in ambient-temperature structures and to 6 Å2 in low-temperature structures, and surprisingly are comparable to values estimated two decades ago. It is well known that B factors are not due to local movements only but reflect several, additional factors from crystal defects, large-scale disorder, diffraction data quality etc. It therefore remains essential to normalize B factors when comparing different crystal structures, although it has clearly been shown that they provide useful information about protein dynamics. Improved, quantitative analyses of raw B factors require novel experimental and computational tools that are able to disaggregate local movements from other features and properties that affect B factors.
Highlights
Data quality is essential in science, and during the last three decades structural biologists have developed several validation protocols aimed at minimizing pitfalls in their results and highlighting possible problems in their structures
Several other validation tools have been developed (Read et al, 2011). They included additional structural features, such as the positions of C -bound H atoms in MolProbity (Chen et al, 2010), which can be considered to be a sort of gold standard in today’s protein 3D model validation, or they address structures solved using a particular experimental method, such as PROCHECK-NMR (Laskowski et al, 1996), which is dedicated to solution NMR structures
The Worldwide Protein Data Bank developed an integrated validation report for protein structures determined using several experimental methods, which became the mandatory quality check for data deposited in the Protein Data Bank (PDB)
Summary
Data quality is essential in science, and during the last three decades structural biologists have developed several validation protocols aimed at minimizing pitfalls in their results and highlighting possible problems in their structures. The basic idea behind PROCHECK is that infrequent structural features, such as for example an anomalous ’/ position in the Ramchandran plot (Carugo & Djinovic-Carugo, 2013), must be examined carefully. They might be genuine and suggesting something interesting, it is more probable that they are mistakes due to poor diffraction data quality or dataprocessing inaccuracy etc. The Worldwide Protein Data Bank (wwPDB) developed an integrated validation report for protein structures determined using several experimental methods (https://validate-rcsb-2.wwpdb.org/), which became the mandatory quality check for data deposited in the Protein Data Bank (PDB)
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