Table 1.
Cryo-EM collection, refinement, and validation statistics
| 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 |