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 |
