Table 1.
Cryo-EM data collection, refinement and validation statistics for mAb1 and mAb2 structures.
| mAb1 full complex | mAb1 | mAb1 | mAb2 full complex | |
|---|---|---|---|---|
| 2 trimers:3 mAbs | Masked | 2 trimers:2 mAbs | 2 trimers:3 mAbs | |
| (EMDB-23293) | (−) | (EMDB-23295) | (EMDB-23296) | |
| (PDB 7LEX) | (−) | (PDB 7LEZ) | (PDB 7LF0) | |
| Data collection and processing | ||||
| Magnification | 130,000 | 130,000 | 130,000 | 130,000 |
| Voltage (kV) | 300 | 300 | 300 | 300 |
| Electron exposure (e–/Å2) | 45.46 | 45.46 | 45.46 | 44.32 |
| Defocus range (μm) | −1.0 to −1.8 | −1.0 to −1.8 | −1.0 to −1.8 | −1.2 to −2.0 |
| Pixel size (Å) | 1.04 | 1.04 | 1.04 | 1.04 |
| Symmetry imposed | C3 | C3 | C1 | C3 |
| Initial particle images (no.) | 94,796 | 94,796 | 94,796 | 52,550 |
| Final particle images (no.) | 37,385 | 77,986 | 16,810 | 52,550 |
| Map resolution (Å) | 3.6 | 3.4 | 4.1 | 3.7 |
| FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 |
| Refinement | ||||
| Initial model used (PDB code) | 6V7C | 6V7C | 6V7C | 6V7C |
| Model resolution (Å) | 3.6 | 3.5 | 4.3 | 3.8 |
| FSC threshold | 0.5 | 0.5 | 0.5 | |
| Map sharpening B factor (Å2) | 106.7 | 134.6 | 77.9 | 109.7 |
| Model composition | ||||
| Non-hydrogen atoms | 25,662 | 25,662 | 21,628 | 25,797 |
| Protein residues | 4554 | 4554 | 3654 | 4542 |
| Ligands | 0 | 0 | 0 | 0 |
| B factors (Å2) | ||||
| Protein | 76.2 | 118.8 | 224.2 | 56.6 |
| Ligand | — | — | — | — |
| R.m.s. deviations | ||||
| Bond lengths (Å) | 0.009 | 0.011 | 0.007 | 0.010 |
| Bond angles (°) | 1.00 | 1.09 | 1.14 | 1.07 |
| Validation | ||||
| MolProbity score | 1.89 | 1.96 | 2.14 | 2.03 |
| Clashscore | 6.42 | 6.9 | 11.4 | 7.5 |
| Poor rotamers (%) | 0.31 | 0.78 | 0.65 | 1.09 |
| Ramachandran plot | ||||
| Favored (%) | 90.4 | 89.3 | 89.2 | 87.8 |
| Allowed (%) | 8.7 | 9.8 | 10.1 | 11.4 |
| Disallowed (%) | 0.89 | 0.89 | 0.66 | 0.80 |
For mAb1, the full complex was not refined in Phenix. For the other complexes, 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.