Table 2A.

Concerns and Unusual Features: Criteria to Flag “Concerns”

Validation criterion	Threshold
Poor overall geometry	Percentile <0.1 for RMS-Z score of bonds, angles, or planes, or percentile <0.1 for fraction outliers of bonds, angles, or planes
Extreme local geometry	Any individual outliers >15σ
Inverted chirality	Incorrect chirality at a Cα (or for a nucleic acid sugar)
Intensity outliers	>10% of reflections have a Wilson probability lower than 10−6
Data labels	Structure amplitudes (F) labeled as intensities (I) or vice versa
Symmetry	Data analysis shows missed symmetry within experimental error but no evidence of twinning, except if depositor indicates that using NCS symmetry produces significantly lower Rfree.
Twinning	Estimated twin fraction >0.2, but no indication that a twin target was used for structure refinement
Translational NCS	Nonorigin peak in native Patterson >75% of origin, and position of peak is consistent with missed centering operator
Incomplete structure	Cα-only coordinates, or no sequence information
Ligand problems	RSR > twice average for protein, poor stereochemistry
Carbohydrates	Nomenclature is inconsistent with structure, or N-glycan chain contains residues that are not known to occur naturally