Table 1. Xenla CMG cryo-EM data collection and processing.
|
Xenla sCMG consensus (EMDB: EMD-18195) |
Xenla dCMGDo consensus (EMDB: EMD-18191) Xenla dCMGDo without ATPase (PDB: 8Q6O) |
Xenla dCMGDo MCM ATPase (EMDB: EMD-18192) Xenla dCMGDo MCM ATPase (PDB: 8Q6P) |
|
|---|---|---|---|
| Data collection and processing | |||
| Nominal magnification | 130,000 | 130,000 | 130,000 |
| Voltage (keV) | 300 | 300 | 300 |
| Electron exposure (e–/Å2) | 33 | 33 | 33 |
| Defocus range (μm) | –1.3 to –3.4 | –1.3 to –3.4 | –1.3 to –3.4 |
| Pixel size (Å) | 0.95 | 0.95 | 0.95 |
| Symmetry imposed | C1 | C2 | C1 |
| Initial particle number | 4,140,303 | 4,140,303 | 4,140,303 |
| Final particle numbers | 137,591 | 100,667 | 144,989 |
| Global map resolution at 0.143 FSC threshold (Å) | 3.03 | 3.14 | 3.53 |
| Map resolution range at 0.5 FSC (Å)a | 2.5–9.5 | 2.7–8.3 | 2.5–8.5 |
| Map sharpening B-factors (Å2) | –91 | –93 | –113 |
| Model refinementb | |||
| Model-map CC (CCmask/CCbox/CCpeaks/CCvolume) | - | 0.81/0.66/0.56/0.81 | 0.78/0.55/0.35/0.77 |
| Model-map FSC, 0.143 threshold (A) (masked/unmasked) | – | 3.1/3.1 | 3.5/3.7 |
| Model-map FSC, 0.5 threshold (Å) (masked/unmasked) |
– | 3.4/3.6 | 3.9/6.4 |
| Model composition | |||
| Non-hydrogen atoms | – | 51,983 | 16,795 |
| Protein residues | – | 6,454 | 2,104 |
| Ligands | – | 10 × Zn2+ | 5 × ATP |
| RMS deviations | |||
| Bond lengths (Å) | – | 0.002 | 0.002 |
| Bond angles (°) | – | 0.492 | 0.484 |
| Mean B-factors (Å2) | |||
| Protein | – | 122.07 | 108.87 |
| Ligands | – | 260.17 | 83.98 |
| Validationc | |||
| MolProbity score | – | 1.35 | 1.35 |
| Clashscore | – | 4.9 | 5.07 |
| Poor rotamers (%) | – | 0.05 | 0.05 |
| CaBLAM outliers (%) | – | 1.20 | 1.48 |
| Ramachandran plotc | |||
| Favored (%) | – | 97.6 | 97.6 |
| Allowed (%) | – | 2.4 | 2.4 |
| Outliers (%) | – | 0.0 | 0.0 |