Table II.
Cryo-EM data collection, refinement, and validation statistics
| C4b-NbB5 PDB 7B2P, EMDB-11989 |
C4b-NbE3 PDB 7B2M, EMDB-11988 |
C4b-NbB12 PDB 7B2Q, EMDB-11990 |
C4b-NbG3 EMDB-11991 |
|
|---|---|---|---|---|
| Data collection and processing | ||||
| Microscope | Talos Arctica | Talos Arctica | Talos Arctica | Talos Arctica |
| Camera | Gatan K2 Summit + GIF | Gatan K2 Summit + GIF | Gatan K2 Summit + GIF | Gatan K2 Summit + GIF |
| Magnification | 130,000 | 130,000 | 130,000 | 130,000 |
| Voltage (kV) | 200 | 200 | 200 | 200 |
| Exposure time frame/total (s) | 0.2/7.2 | 0.2/6.4 | 0.2/6.4 | 0.2/6.4 |
| Number of frames | 36 | 32 | 32 | 32 |
| Electron exposure (e-/ Å2) | 51.7 | 51.7 | 53.9 | 50.5 |
| Defocus range (µm) | −0.8 to −3.0 | −0.8 to −3.0 | −0.8 to −3.0 | −0.8 to −3.0 |
| Pixel size (Å) | 1.029 | 1.029 | 1.029 | 1.029 |
| Micrographs (no.) | 1,032 | 1,396 | 1,453 | 1,658 |
| Initial particle images (no.) | 522,079 | 617,600 | 602,481 | 845,087 |
| Final particles images (no.) | 274,925 | 176,318 | 128,161 | 207,769 |
| Map resolution (Å) 0.143 FSC threshold |
3.43 | 3.39 | 3.76 | 3.96 |
| Map resolution range (Å) | 3.3–5.7 | 3.3–5.1 | 3.6–5.7 | 3.8–6.3 |
| Refinement | ||||
| Model resolution (Å) 0.5 FSC threshold |
3.50 | 3.43 | 3.86 | |
| Map sharpening B factor (Å2) | −125 | −72 | −100 | |
| Model composition | ||||
| Nonhydrogen atoms | 11,690 | 11,664 | 11,612 | |
| Protein residues | 1,509 | 1,506 | 1,495 | |
| Ligands | NAG: 5 | NAG: 4 | NAG: 5 | |
| B factors (Å2) | ||||
| Protein | 71.1 | 69.1 | 75.5 | |
| Ligands | 87.9 | 81.9 | 81.4 | |
| r.m.s.d. | ||||
| Bond lengths (Å) | 0.003 | 0.003 | 0.003 | |
| Bond angles (°) | 0.520 | 0.489 | 0.541 | |
| Validation | ||||
| MolProbity score | 1.78 | 1.59 | 1.85 | |
| Clashscore | 8.12 | 6.41 | 9.07 | |
| Rotamer outliers (%) | 0.0 | 0.0 | 0.0 | |
| Ramachandran plot | ||||
| Favored (%) | 95.12 | 96.44 | 94.70 | |
| Allowed (%) Outliers (%) |
4.88 0.00 |
3.56 0.00 |
5.23 0.07 |
|
r.m.s.d., root mean square deviation.