Table1.
Cryo-EM data collection, refinement, and validation statistics
| TBEV virion (EMD-3752) (PDB 5O6A) | TBEV-Fab 19/1786 (EMD-3754) (PDB 5O6V) | TBEV-Fab 19/1786, pH 5.8 (EMD-3755) | |
|---|---|---|---|
| Data collection and processing | |||
| Magnification | 75,000× | 75,000× | 75,000× |
| Voltage (kV) | 300 | 300 | 300 |
| Electron exposure (e–/Å2) | 22 | 22 | 22 |
| Defocus range (μm) | 0.8–3.8 | 0.8–3.7 | 0.8–3.4 |
| Pixel size (Å) | 1.063 | 1.063 | 1.063 |
| Symmetry imposed | Icosahedral | Icosahedral | Icosahedral |
| Initial particle images (no.) | 19,111 | 12,098 | 4515 |
| Final particle images (no.) | 11,882 | 5929 | 3831 |
| Map resolution (Å) | 3.9 | 3.9 | 19.2 |
| FSC threshold | 0.143 | 0.143 | 0.143 |
| Map resolution range (Å) | 3.8–6.2 | 3.8–7 | 19.2 |
| Refinement | |||
| Initial model used (PDB code) | 1SVB, 3J27 | 1SVB, 3J27 | – |
| Model resolution (Å) | 3.9 | 3.9 | – |
| FSC threshold | 0.143 | 0.143 | – |
| Model resolution range (Å) | ∞−3.9 | ∞–3.9 | – |
| Map sharpening B-factor (Å2) | −115 | −104 | 0 |
| Model composition | – | ||
| Non-hydrogen atoms | 12,942 | 19,346 | – |
| Protein residues | 1689 | 2529 | – |
| Ligands | 3 | 3 | – |
| B-factors (Å2) | – | ||
| Protein | 116.2 | 154.1 | – |
| Ligand | 126.3 | 88.4 | – |
| R.m.s. deviations | – | ||
| Bond lengths (Å) | 0.006 | 0.007 | – |
| Bond angles (°) | 1.06 | 1.15 | – |
| Validation | – | ||
| MolProbity score (percentile) | 1.59 (100) | 1.66 (100) | – |
| Clashscore (percentile) | 2.62 (100) | 3.27 (100) | – |
| Poor rotamers (%) | 0.0 | 0.47 | – |
| Ramachandran plot | – | ||
| Favored (%) | 90.34 | 90.16 | – |
| Allowed (%) | 9.36 | 9.44 | – |
| Disallowed (%) | 0.30 | 0.40 | – |