Table 1.
CryoEM data, structure refinement, and validation
| G115 TCR/CD3/ OKT3 Fab | G115 TCR ECD/ Fab 1 | 9C2 TCR ECD/ Fab 2 | 9C2 TCR ECD/ Fab 3 | |
|---|---|---|---|---|
| Data collection and processing | ||||
| Magnification | 105,000 | 105,000 | 105,000 | 105,000 |
| Voltage (kV) | 300 | 300 | 300 | 300 |
| Electron exposure (e–/Å2) | ~50 | ~40 | ~40 | ~40 |
| Defocus range | −1.0 to −2.2 | −1.0 to -2.2 | −1.0 to -2.2 | −1.0 to −2.2 |
| Pixel size (Å) | 0.839 | 0.839 | 0.839 | 0.839 |
| # of Movies | 15,639 | 8,599 | 8,037 | 5,854 |
| Initial number of particles | 7.2 M | 10.0 M | 5.1 Ma | 3.1 M |
| Particles selected after 2D classification | 1.7 M | 250 K | 64 K | 46 K |
| Final selected particles | 290,758 | 156,210 | 31,918 | 29,351 |
| Symmetry imposed | C1 | C1 | C2 | C2 |
| Map resolution (Å) | 3.27 | 3.21 | 3.45 | 3.46 |
| FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 |
| Refinement | ||||
| Initial Model used | 8ES7 | 8DFW | 4LFH | 4LFH |
| Model composition | ||||
| Non-hydrogen atoms | 8397 | 5222 | 10,480 | 10,522 |
| Protein residues | 1054 | 660 | 1306 | 1310 |
| Ligands | 7 | 4 | 12 | 10 |
| R.m.s. deviations | ||||
| Bond lengths (Å) | 0.002 | 0.003 | 0.002 | 0.003 |
| Bond angles (°) | 0.685 | 0.605 | 0.599 | 0.596 |
| Validation | ||||
| MolProbity score | 2.04 | 1.99 | 2.36 | 2.55 |
| Rotamer outliers (%) | 3.38 | 0.00 | 4.18 | 6.41 |
| Clash score | 6.55 | 12.25 | 9.75 | 11.43 |
| Ramachandran plot | ||||
| Favored (%) | 95.92 | 94.17 | 94.57 | 94.74 |
| Allowed (%) | 4.08 | 5.83 | 5.43 | 5.26 |
| Disallowed (%) | 0.00 | 0.00 | 0.00 | 0.00 |
| Deposition ID | ||||
| PDB | 9CQ4 | 9CQ7 | 9CQ8 | 9CQL |
| EMDB | 45,808 | 45,810 | 45,811 | 45,814 |
aCombined particle counts from 2D template based and Topaz particle picking. Duplicate particles were removed after 2D classification.