Table 1 CryoEM data, structure refinement, and validation
From: Structural characterization of two γδ TCR/CD3 complexes
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 |
