Table 1.
Cryo-EM data collection, refinement and validation statistics of wildtype ScSec and wildtype and mutant TlSec complexes
|
ScSec [Sec62−] (EMD-22770, PDB 7KAH) |
ScSec[C1] (EMD- 22771, PDB 7KAI) |
ScSec[C2] (EMD- 22772, PDB 7KAJ) |
TlSec [Sec62−] (EMD-22773, PDB 7KAK) |
TlSec [Plug-open] (EMD-22774, PDB 7KAL) |
TlSec [Plug-closed] (EMD-22775, PDB 7KAM) |
ΔSec62 TlSec (EMD-22776, PDB 7KAN) |
Δanchor TlSec (EMD- 22777) |
|
|---|---|---|---|---|---|---|---|---|
| Data collection and processing | ||||||||
| Magnification | 64,000x | 64,000x | 64,000x | 36,000x | 36,000x | 36,000x | 36,000x | 64,000x |
| Voltage (kV) | 300 | 300 | 300 | 200 | 200 | 200 | 200 | 300 |
| Electron exposure | ||||||||
| (e−/Å2) | 49.1 | 49.1 | 49.1 | 50.0 | 50.0 | 50.0 | 50.0 | 49.1 |
| Defocus range (μm) | −0.8 to −2.5 | −0.8 to −2.5 | −0.8 to −2.5 | −0.6 to −2.4 | −0.6 to −2.4 | −0.6 to −2.4 | −0.9 to −2.2 | −0.7 to −2.9 |
| Pixel size (Å) | 1.19 | 1.19 | 1.19 | 1.14 | 1.14 | 1.14 | 1.14 | 1.19 |
| Symmetry imposed | C1 | C1 | C1 | C1 | C1 | C1 | C1 | C1 |
| Initial particle | ||||||||
| images (no.) | 2,686,839 | 2,686,839 | 2,686,839 | 1,632,659 | 1,632,659 | 1,632,659 | 546,712 | 229,825 |
| Final particle images | ||||||||
| (no.) | 391,885 | 193,263 | 193,661 | 155,601 | 114,704 | 143,227 | 222,047 | 76,726 |
| Map resolution (Å) | 3.1 | 3.2 | 3.1 | 3.9 | 4.0 | 3.8 | 3.7 | 4.4 |
| FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
| Map resolution range (Å) | 2.6 – 11 | 2.8 – 12 | 2.7 – 12 | 3.4 – 13 | 3.3 – 13 | 3.3 – 12 | 3.3 – 12 | 3.7 – 14 |
| Refinement | ||||||||
| Initial model used | PDB 6N3Q | PDB 7KAH | PDB 7KAH | PDB 7KAN | PDB 7KAN | PDB 7KAN | PDB 6N3Q | - |
| Model resolution (Å) | 3.2 | 3.3 | 3.3 | 4.1 | 4.2 | 4.0 | 4.0 | - |
| FSC threshold | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 | - |
| Map sharpening B factor (Å2) | 86.6 | 80.8 | 75.9 | 110.3 | 90.7 | 105.2 | 127.8 | - |
| Model composition | ||||||||
| Non-hydrogen atoms | 10,495 | 10,718 | 10,712 | 10,438 | 10,794 | 10,921 | 10,661 | - |
| Protein residues | 1,349 | 1,399 | 1,399 | 1,371 | 1,429 | 1,445 | 1,371 | - |
| Ligands | - | - | - | - | - | - | 2 | - |
| B factors (Å2) | ||||||||
| Protein | 73 | 61 | 58 | 117 | 126 | 74 | 30 | - |
| Ligand | - | - | - | - | - | - | 34 | - |
| R.m.s. deviations | ||||||||
| Bond lengths (Å) | 0.003 | 0.003 | 0.003 | 0.002 | 0.002 | 0.003 | 0.003 | - |
| Bond angles (°) | 0.522 | 0.508 | 0.513 | 0.524 | 0.489 | 0.521 | 0.623 | - |
| Validation | ||||||||
| MolProbity score | 1.43 | 1.42 | 1.33 | 1.51 | 1.42 | 1.48 | 1.55 | - |
| Clashscore | 4.61 | 4.14 | 3.87 | 6.33 | 5.62 | 5.60 | 6.18 | - |
| Poor rotamers (%) | 0 | 0 | 0 | 0 | 0 | 0 | 0 | - |
| Ramachandran plot | ||||||||
| Favored (%) | 96.83 | 96.58 | 97.01 | 97.09 | 97.42 | 96.96 | 96.72 | - |
| Allowed (%) | 3.17 | 3.42 | 2.99 | 2.91 | 2.58 | 3.04 | 3.28 | - |
| Disallowed (%) | 0 | 0 | 0 | 0 | 0 | 0 | 0 | - |