Table 1.
Cryo-EM data collection, refinement, and validation statistics.
| EMDB PDB ID |
UTP-bound wt-Nsp15 22610 7K0R |
wt-Nsp15 22611 |
Nsp15 H235A dataset i 22613 |
Nsp15 H235A dataset ii 22612 |
|---|---|---|---|---|
| Data collection and processing | ||||
| Magnification | 36,000 | 36,000 | 45,000 | 45,000 |
| Voltage (kV) | 200 | 200 | 200 | 200 |
| Electron exposure (e−/Å2) | ~54 | ~54 | ~54 | ~54 |
| Defocus range (μm) | −1.0 to −2.5 | −1.0 to −2.5 | −1.0 to −2.5 | −1.0 to −2.5 |
| Pixel size (Å) | 1.187 | 1.187 | 0.932 | 0.932 |
| Scaled pixel size (Å) | 1.145 | 1.145 | 0.8991 | 0.8991 |
| Symmetry imposed | D3 | D3 | D3 | D3 |
| Initial particle images (no.) | 383,271 | 672,879 | 382,348 | 641,748 |
| Final particle images (no.) | 65,393 | 167,106 | 59,703 | 433,403 |
| Map resolution (Å) (FSC = 0.143) | 3.38 | 3.02 | 3.37 | 2.94 |
| Map resolution (Å) (FSC = 0.5) | 3.62 | 3.34 | 3.59 | 3.04 |
| Map resolution range (Å) | 3.3 to 6.2 | 2.6 to 4.9 | 2.8 to 6.0 | 2.3 to 5.8 |
| Refinement | ||||
| Model composition | ||||
| Nonhydrogen atoms | 16,038 | |||
| Protein residues | 2070 | |||
| Ligands | 12 | |||
| B factors (Å2) | ||||
| Protein | 99.24 | |||
| Ligand | 131.77 | |||
| Map-model CC | ||||
| CC (mask) | 0.8335 | |||
| CC (volume) | 0.8287 | |||
| CC (peaks) | 0.7920 | |||
| CC (box) | 0.8794 | |||
| R.M.S. deviations | ||||
| Bond lengths (Å) | 0.009 | |||
| Bond angles (°) | 0.767 | |||
| Validation | ||||
| Molprobity score | 1.23 | |||
| Clashscore | 3.56 | |||
| Poor rotamers (%) | 1.05 | |||
| Ramachandran plot | ||||
| Favored (%) | 97.67 | |||
| Allowed (%) | 2.33 | |||
| Disallowed (%) | 0 | |||