Table 1. Cryo-EM data collection, refinement, and validation statistics.
| Dataset 1 rXkr9 (EMDB-13155) (PDB 7P14) |
Dataset 2 rXkr9 caspase −3 cleaved (EMDB-13157) (PDB 7P16) |
Dataset 3 hXkr8+hBSG |
|
|---|---|---|---|
| Data collection and processing | |||
| Microscope | FEI Titan Krios | FEI Titan Krios | Polara |
| Camera | Gatan K3 GIF | Gatan K3 GIF | Gatan K2 |
| Magnification | 130,000 | 130,000 | 130,000 |
| Voltage (kV) | 300 | 300 | 300 |
| Electron exposure (e–/Å2) | 70 | 70 | 35 |
| Defocus range (μm) | −1.0 to −2.4 | −1.0 to −2.4 | −0.8 to −2.5 |
| Pixel size * (Å) | 0.651 (0.3255) | 0.651 (0.3255) | 1.34 |
| Initial number of micrographs (no.) | 12,396 | 14,929 | 2212 |
| Initial particle images (no.) | 6,252,082 | 8,302,932 | 465,373 |
| Final particle images (no.) | 866,439 | 444,358 | 54,519 |
| Symmetry imposed | C1 | C1 | C1 |
| Map resolution (Å) FSC threshold |
3.66 0.143 |
4.3 0.143 |
15.3 0.143 |
| Map resolution range (Å) | 3.0–6.0 | 3.7–7.0 | |
| Refinement | |||
| Model resolution (Å) FSC threshold |
3.7 0.5 |
4.3 0.5 |
|
| Map sharpening b-factor (Å2) | −199.6 | −229.9 | |
| Model vs Map CC (mask) | 0.76 | 0.74 | |
| Model composition Non-hydrogen atoms Protein residues Ligand |
3796 456 PLC, P5S |
3621 445 PLC |
|
| B factors (Å2) Protein Ligand |
53.43 47.62 |
68.75 49.33 |
|
| R.m.s. deviations Bond lengths (Å) Bond angles (°) |
0.003 0.533 |
0.002 0.453 |
|
| Validation MolProbity score Clashscore Poor rotamers (%) |
1.54 7.45 0.00 |
1.51 7.29 0.00 |
|
| Ramachandran plot Favored (%) Allowed (%) Disallowed (%) |
97.3 2.7 0.00 |
97.48 2.52 0.00 |
*Values in parentheses indicate the pixel size in super-resolution.