Table 2.
Cryo-EM data collection, refinement and validation statistics for the nsp132−RTC conformational states.
| nsp13.1-apo (EMDB-24428) (PDB 7RDZ) | nsp13.1-engaged (EMDB-24427) (PDB 7RDY) | nsp13.1-swiveled (EMDB-24429) (PDB 7RE0) | 1B-open (EMDB-24426) (PDB 7RDX) | |
|---|---|---|---|---|
|
| ||||
| Data collection and processing | ||||
| Magnification | 81,000 | |||
| Voltage (kV) | 300 | |||
| Electron exposure (e–/Å2) | 66 | |||
| Defocus range (μm) | −0.8 to −2.5 | |||
| Pixel size (Å) | 1.07 | |||
| Symmetry imposed | C1 | |||
| Initial particle images (no.) | 315,120 | |||
| Final particle images (no.) | 52,403 | 102,615 | 54,830 | 105,272 |
| Map resolution (Å) | 3.6 | 3.1 | 3.5 | 3.1 |
| FSC threshold 0.143 | ||||
| Map resolution range (Å) | 3.0–7.2 | 2.6–6.9 | 3.0–6.6 | 2.8–6.2 |
| Refinement | ||||
| Initial models used (PDB code) | 6XEZ, 6ZSL | 6XEZ, 6ZSL | 6XEZ, 6ZSL | 6XEZ, 6ZSL |
| Model resolution (Å) | 3.6 | 3.1 | 3.5 | 3.1 |
| FSC threshold 0.5 | ||||
| Map sharpening B factor (Å2) | −78.3 | −84.3 | −75.8 | −82.3 |
| Model composition | ||||
| Non-hydrogen atoms | 21,545 | 21,846 | 21,563 | 21,828 |
| Protein residues | 2,553 | 2,553 | 2,553 | 2,553 |
| Nucleic acid residues (RNA) | 71 | 78 | 71 | 80 |
| Ligands | 13 | 19 | 16 | 19 |
| B factors (Å2) | ||||
| Protein | 173.27 | 99.83 | 151.00 | 89.82 |
| Nucleic acids | 205.08 | 144.22 | 158.63 | 157.87 |
| Ligand | 133.84 | 97.16 | 200.51 | 86.54 |
| R.m.s. deviations | ||||
| Bond lengths (Å) | 0.004 | 0.015 | 0.014 | 0.004 |
| Bond angles (°) | 0.621 | 0.967 | 1.127 | 0.613 |
| Validation | ||||
| MolProbity score | 1.70 | 2.68 | 2.60 | 1.82 |
| Clashscore | 6.09 | 8.05 | 12.57 | 6.30 |
| Poor rotamers (%) | 0.00 | 10.18 | 9.10 | 0.00 |
| Ramachandran plot | ||||
| Favored (%) | 94.76 | 92.40 | 93.01 | 93.66 |
| Allowed (%) | 5.24 | 7.60 | 6.80 | 6.30 |
| Disallowed (%) | 0 | 0 | 0.20 | 0.04 |