Table 1.
Cryo-EM data collection, refinement and validation statistics
| MCM DH | MCM-DDK | |
|---|---|---|
| (EMD-13176, | (EMD-13211, | |
| PDB 7P30) | PDB 7P5Z) | |
| Data collection and processing | ||
| Magnification | 130,000 | |
| Voltage (kV) | 300 | |
| Electron exposure (e–/Å2) | 51.3 | |
| Defocus range (μm) | −2 to −4.1 | |
| Pixel size (Å) | 1.08 | |
| Symmetry imposed | C2 | C1 |
| Initial particle images (no.) | 3,529,085 | 3,529,085 |
| Final particle images (no.) | 238,620 | 149,876 |
| Map resolution (Å) | 2.95 | 3.3 |
| FSC threshold | 0.143 | 0.143 |
| Map resolution range (Å) | 2.7–4.5 | 3.0–8.5 |
| Refinement | ||
| Initial model used (PDB code) | 6F0L (MCM-DH-DNA) | 6F0L (MCM-DH-DNA) |
| 5BK4 (MCM-DH-DNA) | 5BK4 (MCM-DH-DNA) | |
| 6EYC (MCM-DH-DNA) | 6EYC (MCM-DH-DNA) | |
| 6YA7 (Cdc7-Dbf4) | ||
| 3QBZ (Dbf4 BRCT) | ||
| Model resolution (Å) | 3.1 | 3.6 |
| FSC threshold | 0.5 | 0.5 |
| Map sharpening B factor (Å2) | ResolveCryo-EM | −10 |
| Model composition | ||
| Nonhydrogen atoms | 62,909 | 67,425 |
| Protein residues | 7,766 | 8,315 |
| Ligands | 30 (2 ATP, 8 ADP, 10 Mg2+, 10 Zn 2+) | 31 (2 ATP, 8 ADP, 10 Mg2+, 11 Zn 2+) |
| B factors (Å2) | ||
| Protein | 3.37/73.99/27.47 | 77.38/416.67/133.20 |
| Ligand | 8.86/93.94/27.55 | 102.71/268.16/126.96 |
| R.m.s. deviations | ||
| Bond lengths (Å) | 0.003 | 0.003 |
| Bond angles (°) | 0.551 | 0.568 |
| Validation | ||
| MolProbity score | 1.40 | 1.77 |
| Clashscore | 4.34 | 10.77 |
| Poor rotamers (%) | 0.06 | 0.03 |
| Ramachandran plot | ||
| Favored (%) | 96.88 | 96.62 |
| Allowed (%) | 3.08 | 3.30 |
| Disallowed (%) | 0.04 | 0.09 |