Table 2.
Cryo-EM data collection, refinement and validation statistics for mAb3, mAb4 and mAb5 structures.
| mAb3 | mAb4-HiRes | mAb4—full | mAb5 | |
|---|---|---|---|---|
| 2 trimers:3 mAbs | (−) | 2 trimers:2 mAbs | 1 trimer:3 mAbs | |
| (EMDB-23297) | (−) | (EMDB-23298) | (EMDB-23294) | |
| (PDB 7LF1) | (PDB 7LF2) | (PDB 7LEY) | ||
| Data collection and processing | ||||
| Magnification | 130,000 | 130,000 | 130,000 | 130,000 |
| Voltage (kV) | 300 | 300 | 300 | 300 |
| Electron exposure (e–/Å2) | 44.47 | 44.47 | 44.47 | 45.44 |
| Defocus range (μm) | −1.0 to −2.0 | −1.0 to −2.0 | −1.0 to −2.0 | −1.0 to −2.0 |
| Pixel size (Å) | 1.04 | 1.04 | 1.04 | 1.04 |
| Symmetry imposed | C3 | C3 | C3 | C3 |
| Initial particle images (no.) | 87,069 | 41,176 | 41,176 | 80,738 |
| Final particle images (no.) | 52,241 | 31,797 | 31,797 | 44,345 |
| Map resolution (Å) | 4.0 | 3.5 | 3.7 | 3.1 |
| FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 |
| Refinement | ||||
| Initial model used (PDB code) | 6V7C | 6V7C | 6V7C | 6V7C |
| Model resolution (Å) | 4.3 | 3.8 | 4.0 | 3.2 |
| FSC threshold | 0.5 | 0.5 | 0.5 | 0.5 |
| Map sharpening B factor (Å2) | 131.8 | 117.9 | 108.4 | 89.0 |
| Model composition | ||||
| Non-hydrogen atoms | 34,517 | 33,798 | 33,798 | 2265 |
| Protein residues | 4548 | 4452 | 4452 | 4902 |
| Ligands | 0 | 0 | 0 | 0 |
| B factors (Å2) | ||||
| Protein | 299 | 149 | 363 | 73.6 |
| Ligand | — | — | — | — |
| R.m.s. deviations | ||||
| Bond lengths (Å) | 0.006 | 0.011 | 0.007 | 0.010 |
| Bond angles (°) | 1.05 | 1.09 | 1.14 | 1.07 |
| Validation | ||||
| MolProbity score | 2.20 | 2.04 | 2.15 | 2.24 |
| Clashscore | 12.0 | 5.4 | 11.2 | 7.2 |
| Poor rotamers (%) | 0.16 | 0.68 | 0.16 | 0.79 |
| Ramachandran plot | ||||
| Favored (%) | 86.7 | 88.4 | 89.0 | 87.9 |
| Allowed (%) | 12.9 | 11.2 | 10.9 | 11.4 |
| Disallowed (%) | 0.40 | 0.39 | 0.14 | 0.67 |
The relatively low values for the CC Mask, Volume and Peaks observed for the refinement of the full complex reflect the high degree of variability in the resolution range.