Table 1 Cryo-EM data collection, refinement and validation statistics
ACNDV pH 7.5 (EMDB-15295) (PDB 8AAC) | ACNDV pH 5.5 (EMDB-16371) (PDB 8C0O) | ACNDV pH 7.5 | ACNDV pH 5.5 | ACNDV pH 5.5 shifted to pH 7.5 | |
|---|---|---|---|---|---|
Data collection and processing | |||||
Magnification | 130,000 | 166,600 | 129,000 | 129,000 | 129,000 |
Voltage (kV) | 300 | 300 | 300 | 300 | 300 |
Electron exposure (e–/Å2) | 76 | 55 | 77 | 77 | 77 |
Defocus range (μm) | −0.5 to −2 | −0.2 to −2 | −1 to −2.6 | −1 to −2.6 | −1 to −2.6 |
Pixel size (Å) | 1.07 | 0.845 | 1.087 | 1.087 | 1.087 |
Symmetry imposed | I | I | I | I | I |
Initial particle images (no.) | 375,654 | 215,225 | 146,077 | 346,287 | 257,179 |
Final particle images (no.) | 70,868 | 77,129 | 38,355 | 141,485 | 61,336 |
Map resolution (Å) | 3.7 | 3.9 | 4.1 | 3.8 | 3.9 |
FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
Map resolution range (Å) | 3.2–8.0 | 3.4–7.9 | 3.4–6.3 | 3.4–6.7 | 3.4–6.4 |
Refinement | |||||
Initial model used (PDB code) | de novo | de novo | |||
Model resolution (Å) | 3.9 | 4.2a | |||
FSC threshold | 0.5 | 0.5 | |||
Map sharpening B factor (Å2) | −190 | −280 | |||
Model composition | |||||
Non-hydrogen atoms | 198,540 (1103 per chain) | 197,460 (1097 per chain) | |||
Protein residues | 137 per chain | 136 per chain | |||
B factors (Å2) | |||||
Protein | 68.73 | 55.67 | |||
R.m.s. deviations | |||||
Bond lengths (Å) | 0.008 | 0.005 | |||
Bond angles (°) | 1.06 | 1.144 | |||
Validation | |||||
MolProbity score | 0.89 | 1.24 | |||
Clashscore | 1.47 | 2.04 | |||
Poor rotamers (%) | 0 | 0.9 | |||
Ramachandran plot | |||||
Favored (%) | 98.02 | 96.05 | |||
Allowed (%) | 1.98 | 3.95 | |||
Disallowed (%) | 0 | 0 | |||
