Table 1.
Cryo-EM data collection, refinement, and validation statistics.
| HIV-1AD8 Env (EMD-28953) (8FAD) |
HIV-1AE2 Env (EMD-28954) (8FAE) |
|
|---|---|---|
| Data collection and processing | ||
| Magnification | 105,000 | 105,000 |
| Voltage (kV) | 300 | 300 |
| Electron exposure (e/Å) | 54 | 52/56/62 |
| Defocus range (μm) | −1.0 to −2.7 | −1.0 to −3.0 |
| Pixel size (Å) | 0.685 | 0.825 |
| Symmetry imposed | C1 | C1 |
| Initial particle images (no.) | 365,824 | 1,209,493 |
| Final particle images (no.) | 37,797 | 140,035 |
| Map resolution (Å) | 4.1 | 3.8 |
| FSC threshold | 0.143 | 0.143 |
| Map resolution range (Å) | 3.6–8 | 3.6–8 |
| Refinement | ||
| Initial model used (PDB code) | 7N6U | 7N6U |
| Model resolution (Å) | 4.0 | 3.9 |
| FSC threshold | 0.143 | 0.143 |
| Model resolution range (Å) | 3.5–8 | 3.5–8 |
| Map sharpening B factor (Å2) | −80 | −80 |
| Model composition | ||
| Non-hydrogen atoms | 16,210 | 17,693 |
| Protein residues | 1797 | 1832 |
| Ligands | 145 | 250 |
| B factors (Å2) | ||
| Protein | 86.11 | 184.36 |
| Ligands | 133.64 | 105.59 |
| R.m.s. deviations | ||
| Bond lengths (Å) | 0.010 | 0.012 |
| Bond angles (degree) | 1.471 | 1.596 |
| Validation | ||
| MolProbity score | 2.51 | 2.55 |
| Clashscore | 10.10 | 8.21 |
| Poor rotamers (%) | 3.58 | 5.71 |
| Ramachandran plot | ||
| Favored (%) | 89.48 | 90.57 |
| Allowed (%) | 9.57 | 8.49 |
| Disallowed (%) | 0.96 | 0.94 |