Table 1 Cryo-EM data collection, refinement and validation statistics
From: Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block interaction with ACE2
Data collection and processing | ||
Magnification | 105,000 | 81,000 |
Voltage (kV) | 300 | 300 |
Electron exposure (e−/Å2) | 43 | 46 |
Defocus range (μm) | 0.8–2.6 | 1.0–3.0 |
Pixel size (Å/pixel) (super-resolution) | 0.415 | 0.53 |
Symmetry imposed | C1 | C1 |
Initial particle images (no.) | 596,825 | 786,392 |
Final particle images (no.) | 305,513 | 126,938 |
Map resolution (Å) | 3.3 | 3.7 |
FSC threshold | 0.143 | 0.143 |
Map resolution range (Å) | 3.2–9.7 | 3.7–7.0 |
Refinementa | ||
Initial model used | PDB 6VXX | PDB 6Z43 |
Model resolution (Å) | 3.4 | 3.7 |
FSC threshold | 0.143 | 0.143 |
Model resolution range (Å) | 3.3–6.0 | 3.7–6.0 |
Map sharpening B factor (Å2) | −117 | −114 |
Model composition | ||
Non-hydrogen atoms | 26,725 | 26,960 |
Protein residues | 3,351 | 3,419 |
B factors (Å2) | ||
Protein | 119 | 183 |
R.m.s. deviations | ||
Bond lengths (Å) | 0.005 | 0.006 |
Bond angles (°) | 0.58 | 1.28 |
Validation | ||
MolProbity score | 1.43 | 1.53 |
Clashscore | 8.7 | 5.5 |
Poor rotamers (%) | 0.1 | 0.9 |
Ramachandran plot | ||
Favored (%) | 94.8 | 96.4 |
Allowed (%) | 5.1 | 3.6 |
Disallowed (%) | 0.1 | 0.0 |
