Extended Data Table 2 |.
Statistics of cryo-EM data collection, refinement and validation
| 1:2 model NCP-NSD3C-E1181K/T1232A EMDB-30456 PDB: 7CRQ |
1:1 model NCP-NSD3C-E1181K/T1232A EMDB-30455 PDB: 7CRP |
1:1 model NCP-NSD3C EMDB-30457 PDB: 7CRR |
1:1 model NCP-NSD2C-E1099K/T1150A EMDB-30453 PDB: 7CRO |
|
|---|---|---|---|---|
| Data collection and processing | ||||
| Magnification | 130,000 | 130,000 | 130,000 | 130,000 |
| Voltage (kV) | 300 | 300 | 300 | 300 |
| Electron exposure (e−/Å2) | 50 | 50 | 50 | 50 |
| Defocus range (μm) | 1.2–2.2 | 1.2–2.2 | 1.2–2.2 | 1.2–2.2 |
| Pixel size (Å) | 1.08 | 1.08 | 1.08 | 1.08 |
| Symmetry imposed | C1 | C1 | C1 | C1 |
| Initial particle image (no.) | 2.28 M | 2.28 M | 1.11 M | 910 K |
| Final particle image (no.) | 283 K | 215 K | 61 K | 71.1 K |
| Map resolution (Å) | 3.15 | 3.20 | 3.48 | 3.75 |
| FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 |
| Map resolution range (Å) | 2.4–4.8 | 2.4–4.8 | 3.1–6.0 | 3.5–8.0 |
| Refinement | ||||
| Map sharpening B factor (Å2) | −114 | −119 | −119 | −160 |
| Model composition | ||||
| Protein residues | 1,226 | 1,002 | 1,002 | 999 |
| DNA residues | 336 | 336 | 336 | 336 |
| Ligands (SAM and Zn2+) | 2 SAM, 6 Zn2+ | 1 SAM, 3 Zn2+ | 1 SAM, 3 Zn2+ | 1 SAM, 3 Zn2+ |
| R.m.s. deviations | ||||
| Bond lengths (Å2) | 0.006 | 0.006 | 0.007 | 0.006 |
| Bong angles (°) | 0.689 | 0.713 | 0.703 | 0.692 |
| Validation | ||||
| MolProbity score | 1.9 | 1.81 | 2.03 | 1.97 |
| Clash score | 7.18 | 5.86 | 9.11 | 8.95 |
| Poor rotamers (%) | 0.39 | 0.24 | 0.24 | 0 |
| Ramachandran plot | ||||
| Favored (%) | 91.34 | 91.85 | 90.21 | 91.72 |
| Allowed (%) | 8.58 | 8.15 | 9.79 | 8.28 |
| Disallowed (%) | 0.08 | 0 | 0 | 0 |