Table 2.
Local and global structure validation measures
| Validation measure | Local | Global | Reference | |
|---|---|---|---|---|
| Quality and fit of ligand | Real Space Correlation Coefficient (RSCC) | ● | ● | N/A |
| Real Space R-value (RSR) | ● | ● | [43, 44] | |
| Real Space Observed Density Z-Score (RSZO) | ● | ● | [40] | |
| Occupancy-Weighted Average B-factor (OWAB) | ● | [15, 20] | ||
| S score | ● | [15] | ||
| Q score | ● | [13] | ||
| Local Ligand Density Fit (LLDF) | ● | http://bit.ly/1si1ZeL | ||
| deviation of bond lengths | ● | [35] | ||
| deviation of bond angles | ● | |||
| Quality of model and data | R-value | ● | N/A | |
| R-free | ● | [38] | ||
| CC* | ● | [39] | ||
| Real Space R-value (RSR) | ● | ● | [44] | |
| Diffraction-data Precision Indicator (DPI) | ● | [90] | ||
| Quality of model and stereochemistry | RMSD/Z bond lengths | ● | ● | [35] |
| RMSD/Z bond angles | ● | ● | ||
| G-factor | ● | [91] | ||
| Clashscore | ● | ● | [53, 54] | |
| Ramachandran outliers | ● | [92] | ||
| Other measures of model and data quality | Volumetric packing scores | ● | ● | [93, 94] |
| B-factor | ● | ● | [95, 96] | |
| Resolution | ● | N/A |
Local validation measures are metrics used to validate the quality of the ligand model, and global validation measures are used to assess the overall quality of the protein–ligand model. Many local measures can also be averaged to provide a (less informative) global measure