Table 2.
Cryo-EM data collection, refinement and validation statistics
| Closed conformation (EMDB-18120) (PDB 8Q3B) | Stalka (EMDB-18264) | Open conformationa (EMD-18163) | Open conformation (composite map)a (EMDB-18129) (PDB 8Q3K) | |
|---|---|---|---|---|
| Data collection and processingb | ||||
| Magnification | 105,000 | - | - | - |
| Voltage (kV) | 300 | - | - | - |
| Electron exposure (e-/Å2) | 48.152 | - | - | - |
| Defocus range (μm) | 1.5 - 2.7 | - | - | - |
| Pixel size (Å) | 0.828 | - | - | - |
| Symmetry imposed | C1 | - | - | - |
| Initial particle images (no.) | 4,842,857 | - | - | - |
| Final particle images (no.) | 467,000 | 467.519 | 352,192 | n/a |
| Map resolution (Å) | 2.69 | 2.99 | 2.92 | n/a |
| FSC threshold | 0.143 | 0.143 | 0.143 | |
| Map resolution range (Å) | n/ac | 2.84 - 6.55 | 2.82 - 5.72 | n/a |
| Refinement | ||||
| Initial model used (PDB code) | none | - | - | 8Q3B |
| Model resolution (Å) | 2.9 | - | - | 3.0 |
| FSC threshold | 0.143 | 0.143 | ||
| Model resolution range (Å) | 2.7 - 3.0 | - | 2.8 - 3.2 | |
| Map sharpening B factor (Å2) | 113.15 | 70.28 | 84.87 | n/a |
| Model composition | - | - | ||
| Protein residues | 3724 | 3633 | ||
| Ligands | 1 Mg, 6 Zn | 1 Mg, 6 Zn | ||
| B factors (Å2) | - | - | ||
| Protein | 83.16 | 94.15 | ||
| Ligand | 140.13 | 174.54 | ||
| R.m.s. deviations | - | - | ||
| Bond lengths (Å) | 0.003 | 0.003 | ||
| Bond angles (°) | 0.552 | 0.511 | ||
| Validation | - | - | ||
| MolProbity score | 1.23 | 1.29 | ||
| Clashscore | 4.62 | 5.45 | ||
| Poor rotamers (%) | 0.46 | 0.22 | ||
| Ramachandran plot | - | - | ||
| Favoured (%) | 98.05 | 98.05 | ||
| Allowed (%) | 1.95 | 1.95 | ||
| Disallowed (%) | 0.00 | 0.00 | ||
aThe stalk (EMDB-18264) was obtained from the multibody refinement of the closed conformation and combined with the open conformation (EMDB-18163) to produce the composite map (EMDB-18129). Only the latter was used for the refinement.
bAll maps were obtained from the same dataset.
cThe local resolution evaluation was carried out in cryoSPARC which does not provide this information.