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. 2025 Jan 2;16:318. doi: 10.1038/s41467-024-55467-5

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 (e2) ~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.