Table 1.
Cryo-EM data collection, refinement and validation statistics
| RNCRodZ•SecA (EMDB-10073, PDB 6S0K) | SecA (local refinement) (EMDB-10074) | |
|---|---|---|
| Data collection and processing | ||
| Magnification | 100,719 | 100,719 |
| Voltage (kV) | 300 | 300 |
| Electron exposure (e–/Å2) | 40 | 40 |
| Defocus range (μm) | 1.5 – 2.8 | 1.5 – 2.8 |
| Pixel size (Å) | 1.39 | 1.39 |
| Symmetry imposed | C1 | C1 |
| Initial particle images (no.) | 2,613,025 | 2,613,025 |
| Final particle images (no.) | 37,334 | 37,334 |
| Map resolution (Å) | 3.1 | 5.7 |
| FSC threshold | 0.143 | 0.143 |
| Map resolution range (Å) | 2.9 – 9.5 | 5.5 – 9.5 |
| Refinement | ||
| Initial model used (PDB code) | 5GAG, 2FSF, 2VDA | |
| Model resolution (Å) | 3.3 | |
| FSC threshold | 0.5 | |
| Model resolution range (Å) | – | |
| Map sharpening B factor (Å2) | –130.53 | |
| Model composition | ||
| Non-hydrogen atoms | 98,708 | |
| Protein residues | 4,384 | |
| Nucleic acid residues | 3,006 | |
| Ligands | 69 | |
| B factors (Å2) | ||
| Protein | 148.63 | |
| Nucleotide | 95.06 | |
| Ligand | 60.40 | |
| R.m.s. deviations | ||
| Bond lengths (Å) | 0.005 | |
| Bond angles (°) | 0.776 | |
| Validation | ||
| MolProbity score | 1.52 | |
| Clashscore | 4.21 | |
| Poor rotamers (%) | 0.73 | |
| Ramachandran plot | ||
| Favored (%) | 95.44 | |
| Allowed (%) | 4.28 | |
| Disallowed (%) | 0.28 |