Table 2.
Cryo-EM data collection, refinement and validation statistics of mutant ScSec complexes
| PM ScSec [Sec62−] (EMD-22778, PDB 7KAO) |
PM ScSec [C1] (EMD- 22779, PDB 7KAP) |
PM ScSec [C2] (EMD-22780, PDB 7KAQ) |
FN3mut ScSec [Sec62−] (EMD- 22781, PDB 7KAR) |
FN3mut ScSec [Sec62+] (EMD- 22782, PDB 7KAS) |
PM/FN3mut ScSec [Sec62−] (EMD- 22783, PDB 7KAT) |
PM/FN3mut ScSec [Sec62+] (EMD- 22784, PDB 7KAU) |
FN3mut/ Δ210-216 ScSec (EMD- 22787, PDB 7KB5) |
|
|---|---|---|---|---|---|---|---|---|
| Data collection and processing | ||||||||
| Magnification | 64,000x | 64,000x | 64,000x | 64,000x | 64,000x | 64,000x | 64,000x | 45,000x |
| Voltage (kV) | 300 | 300 | 300 | 300 | 300 | 300 | 300 | 200 |
| Electron exposure | ||||||||
| (e−/Å2) | 48.8 | 48.8 | 48.8 | 49.1 | 49.1 | ~48–49 | ~48–49 | 63 |
| Defocus range (μm) | −1.0 to −2.7 | −1.0 to −2.7 | −1.0 to −2.7 | −0.8 to −2.7 | −0.8 to −2.7 | −1.1 to −2.2 | −1.1 to −2.2 | −0.7 to −2.0 |
| Pixel size (Å) | 1.15 | 1.15 | 1.15 | 1.19 | 1.19 | 1.19 | 1.19 | 0.9 |
| Symmetry imposed | C1 | C1 | C1 | C1 | C1 | C1 | C1 | C1 |
| Initial particle images (no.) | 195,915 | 195,915 | 195,915 | 1,274,219 | 1,274,219 | 267,541 | 267,541 | 2,270,392 |
| Final particle images (no.) | 35,573 | 17,341 | 16,679 | 82,671 | 119,420 | 32,704 | 54,139 | 257,231 |
| Map resolution (Å) | 4.0 | 4.1 | 4.0 | 4.0 | 3.9 | 4.4 | 4.0 | 3.8 |
| FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
| Map resolution range (Å) | 3.5 - 14 | 3.5 - 17 | 3.5 - 16 | 3.4 - 14 | 3.3 - 18 | 3.7 - 19 | 3.4 - 16 | 3.2 - 13 |
| Refinement | ||||||||
| Initial model used | PDB 7KAH | PDB 7KAI | PDB 7KAJ | PDB 7KAH | PDB 7KAR | PDB 7KAH | PDB 7KAT | PDB 7KAH |
| Model resolution (Å) | 4.2 | 4.2 | 4.2 | 4.2 | 4.1 | 4.5 | 4.2 | 4.0 |
| FSC threshold | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 |
| Map sharpening B factor (Å2) | 50.9 | 39.3 | 32.9 | 74.8 | 73.8 | 59.3 | 58.1 | 119.3 |
| Model composition | ||||||||
| Non-hydrogen atoms | 10,502 | 10,715 | 10,753 | 10,435 | 10,616 | 10,431 | 10,711 | 9,777 |
| Protein residues | 1,349 | 1,398 | 1,402 | 1,341 | 1,385 | 1,340 | 1,396 | 1,252 |
| Ligands | - | - | - | - | - | - | - | - |
| B factors (Å2) | ||||||||
| Protein | 152 | 178 | 187 | 117 | 64 | 255 | 125 | 126 |
| Ligand | - | - | - | - | - | - | - | - |
| R.m.s. deviations | ||||||||
| Bond lengths (Å) | 0.003 | 0.003 | 0.002 | 0.003 | 0.004 | 0.002 | 0.003 | 0.004 |
| Bond angles (°) | 0.520 | 0.519 | 0.494 | 0.581 | 0.596 | 0.501 | 0.533 | 0.626 |
| Validation | ||||||||
| MolProbity score | 1.48 | 1.49 | 1.46 | 1.58 | 1.63 | 1.37 | 1.53 | 1.71 |
| Clashscore | 7.65 | 7.87 | 7.39 | 7.84 | 6.69 | 6.71 | 6.26 | 7.3 |
| Poor rotamers (%) | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Ramachandran plot | ||||||||
| Favored (%) | 97.74 | 97.74 | 97.75 | 97.19 | 96.17 | 98.10 | 96.86 | 95.60 |
| Allowed (%) | 2.26 | 2.26 | 2.25 | 2.81 | 3.83 | 1.90 | 3.14 | 4.40 |
| Disallowed (%) | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |