Table 1.

Key Validation Metrics Reported in the wwPDB Structure Validation Reports and Used for Percentile Rank Calculation

Metric	Details	Software Package and References
Rfree	cross-validation of goodness of fit between the model and the experimental diffraction data not used for refinement. Applicable to crystallographic structures	DCC (Yang et al., 2016)
Clashscore	number of too-close contacts in an entry normalized per 1,000 atoms	MolProbity (Chen et al., 2010)
Ramachandran outliers	fraction of polypeptide residues deemed to have very unusual backbone conformation (<0.5% of those observed in a high-quality reference set)	MolProbity (Chen et al., 2010), Maxit (Z.F., https://sw-tools.rcsb.org/apps/MAXIT)
Side-chain outliers	fraction of polypeptide residues in non-rotameric side-chain conformations (<0.5% of those observed in a high-quality reference set)	MolProbity (Chen et al., 2010)
RSRZ outliers	fraction of polypeptide and/or polynucleotide residues that do not fit the electron density well when compared with other instances of the same residues in structures at similar resolution. Applicable to crystallographic structures	EDS (Kleywegt et al., 2004)
RNA backbone	average score over all RNA nucleotides in the entry indicating the quality of the observed RNA backbone conformation	MolProbity (Chen et al., 2010)