Table 1 Cryo-EM collection, refinement, and validation statistics
From: Tumor-agnostic cancer therapy using antibodies targeting oncofetal chondroitin sulfate
Homotypic interacting B1 Fabs bound to chondroitin sulfate A (EMDB-17362) (PDB-8P2E) | |
|---|---|
Data collection and processing | |
Microscope | Titan Krios |
Camera | Falcon III |
Magnification | 130,000 |
Voltage (kV) | 300 |
Electron exposure (e–/Å2) | 40 |
Defocus range (μm) | −1.2 to −2.8 |
Pixel size (Å) | 0.832 |
Symmetry imposed | C1 |
Initial particle images (no.) | 1,257,314 |
Final particle images (no.) | 235,115 |
Map resolution (Å) FSC threshold (0.143) | 3.3 (based on 3DFSC) |
Map sharpening B factor (Å2) | 107.8 |
FSC model (0/0.143/0.5) | 2.8/3.2/3.8 (Masked) |
Refinement | |
Initial model used (PDB code) | N/A (Alphafold) |
Model composition | |
Non-hydrogen atoms | 12,786 |
Ligands | N/A |
R.m.s. deviations | |
Bond lengths (Å) | 0.018 |
Bond angles (°) | 1.693 |
Validation | |
MolProbity score | 1.33 |
Clashscore | 5.1 |
Poor rotamers (%) | 0.14 |
Ramachandran plot | |
Favored (%) | 97.73 |
Allowed (%) | 1.92 |
Disallowed (%) | 0.36 |
Cβ outliers (%) | 0 |
Model vs data CC mask/box/peaks/volume | 0.72/0.82/0.64/0.7 |
