Table 1. MolProbity statistics comparing the cryo-EM map-derived models before and after real space optimization (RSO) and the X-ray structure (PDB id: 1JS9).
| Asymmetric unit | Three subunits | Cryo-EM model 477 residues at 3.8 Å resolution after RSO | Cryo-EM model 477 residues at 3.8 Å resolution before RSO | X-ray (PDB id:1JS9) 503 residues at 3.4 Å resolution | |||
|---|---|---|---|---|---|---|---|
| Density agreement | Correlation coefficient | 0.84 | 0.76 | 0.68 | |||
| All-atom contacts | Clash score (all atoms)* | 13.35 | 97th percentile | 16.02 | 97th percentile | 31.77 | 78th percentile |
| Protein geometry | Poor rotamers | 0 | 0% | 172 | 46% | 181 | 49% |
| Ramachandran outliers | 12 | 2.55% | 48 | 10% | 44 | 9% | |
| Ramachandran favored | 434 | 92.14% | 345 | 69% | 351 | 71% | |
| Molprobity score* | 2.11 | 100th percentile | 3.82 | 46th percentile | 4.1 | 21st percentile | |
| Cβ deviations | 0 | 0% | 0 | 0% | 0 | 0% | |
| Bad backbone bonds | 0 | 0% | 1 | 0.05% | 0 | 0% | |
| Bad backbone angles | 0 | 0% | 8 | 0.32% | 5 | 0.2% | |
Cryo-EM, electron cryo-microscopy.
A complete asymmetric unit was analyzed, but the number of amino acids varies due to resolvability in the density map. In addition, cross-correlation values were computed between the map and the model for the asymmetric unit. Percentiles were calculated based on the deposited structures at the reported resolution.
*Percentile values based on deposited structures at the reported resolution.