TABLE 1.
Cryo-EM data collection, refinement and validation statistics
| Vif176Δ114–157–A3FCTDm-40-CBFβ151 (EMD-9380, PDB 6NIL) | Vif176–A3FCTDm-40-CBFβ187 (EMD-9381) | ||
|---|---|---|---|
| Data collection and processing | 1 | 2/3 | 1 |
| Magnification | 130,000 | 130,000 | |
| Voltage (kV) | 300 | 300 | |
| Electron exposure (e–/Å2) | ~56 | 61/56 | 59 |
| Defocus range (μm) | −1.2 to −2.9 | −1.7 to −3.7/ −1.5 to −3.2 | −0.9 to −2.9 |
| Pixel size (Å) | 1.05 | 1.05 | |
| Stage tilting (°) | 0 | −30/−30 | −30 |
| Symmetry imposed | D2 | D2 | |
| Initial particle images (no.) | 1243243 (untilt) / 1197365 (tilt) | 1140691 | |
| Final particle images (no.) | 337256 | 165629 | |
| Map resolution (Å) | 3.9 | 5 | |
| FSC threshold | 0.143 | 0.143 | |
| Map resolution range (Å) | 3.7–4.6 | - | |
| Refinement | |||
| Initial model used (PDB code) | 4N9F, 3WUS | - | |
| Model resolution (Å) | 3.9 | - | |
| FSC threshold | 0.5 | ||
| Model resolution range (Å) | 3.9–113.4 | - | |
| Map sharpening B factor (Å2) | −223 | −359 | |
| Model composition | |||
| Nonhydrogen atoms | 15216 | - | |
| Protein residues | 1800 | - | |
| Ligands | Zn, 4 | - | |
| B factors (Å2) | |||
| Protein | 113 | - | |
| Ligand | 343 | - | |
| R.m.s. deviations | |||
| Bond lengths (Å) | 0.005 | - | |
| Bond angles (°) | 1.0 | - | |
| Validation | |||
| MolProbity score | 1.67 | - | |
| Clashscore | 3 | - | |
| Poor rotamers (%) | 0.99 | - | |
| Ramachandran plot | |||
| Favored (%) | 90.4 | - | |
| Allowed (%) | 9.6 | - | |
| Disallowed (%) | 0 | - | |