Table 1 Cryo-EM data collection, refinement and validation statistics
From: Trapping the HIV-1 V3 loop in a helical conformation enables broad neutralization
bnD.9 in complex with BG505.SOSIP | |
|---|---|
Data collection and processing | |
Magnification | ×81,000 |
Voltage (kV) | 300 |
Electron exposure (e–/Å2) | 41.92 |
Defocus range (μm) | –0.8/–2.5 |
Pixel size (Å) | 1.07 |
Symmetry imposed | C1 |
Initial particle images (no.) | 406,207 |
Final particle images (no.) | 115,325 |
Map resolution (Å) | 3.87 |
FSC threshold | 0.143 |
Map resolution range (Å) | 3.8–20 |
Refinement | |
Initial model used (PDB code) | 5VN3 |
Model resolution (Å) | 3.93 |
FSC threshold | 0.143 |
Map sharpening B factor (Å2) | 119.2 |
Chimera CC | 0.83 |
EMRinger score | 1.64 |
Model composition | |
Non-hydrogen atoms | 20,555 |
Protein residues | 2,483 |
Ligands | 95 |
B factors (Å2), mean | |
Protein | 107.62 |
Ligand | 93.42 |
R.m.s. deviations | |
Bond lengths (Å) | 0.005 |
Bond angles (°) | 4.51 |
Validation | |
MolProbity score | 1.54 |
Clashscore | 4.51 |
Poor rotamers (%) | 0 |
Ramachandran plot | |
Favored (%) | 95.5 |
Allowed (%) | 4.5 |
Disallowed (%) | 0 |
