Table 2.
Statistics of data collection and processing
| T = 3 PvNV-LP (EMD-9576) (PDB 6AB6) | T = 1 PvNV-LP (EMD-6999) (PDB 6AB5) | |
|---|---|---|
| Data collection and processing | ||
| Magnification | 59,000× | |
| Voltage (kV) | 300 | |
| Electron exposure (e–/Å2) | 40 | |
| Defocus range (μm) | −1.25 to −2.75 | |
| Pixel size (Å) | 1.12 | |
| Symmetry imposed | Icosahedral sym. | Icosahedral sym. |
| Initial model used (ID) | EMD-3655 | PDB 2ZZQ |
| Applied low-pass filter | 60 | 40 |
| Initial particle images (no.) | 42,751 | 476,834 |
| Final particle images (no.) | 8596 | 70,543 |
| Map resolution (Å) | 3.5 | 3.7 |
| FSC threshold | 0.143 | 0.143 |
| Refinement | ||
| Resolution (Å) | 3.5 | 3.7 |
| Map sharpening B factor (Å2) | −195 | −273 |
| Model composition | ||
| Nonhydrogen atoms | – | – |
| Protein residues | – | 489 |
| Ligands | – | – |
| B factors (Å2) | ||
| Protein | 70.36 | 61.55 |
| Ligand | 96.20 | – |
| R.m.s. deviations | ||
| Bond lengths (Å) | 0.0077 | 0.01 |
| Bond angles (°) | 1.20 | 1.18 |
| Validation | ||
| MolProbity score | 1.61 | 1.61 |
| Clashscore | 4.69 | 4.51 |
| Poor rotamers (%) | 0.48 | 0.37 |
| Ramachandran plot | ||
| Favored (%) | 94.7 | 94.4 |
| Allowed (%) | 5.3 | 5.6 |
| Disallowed (%) | 0.0 | 0.0 |