Table 2.
Cryo-EM data collection, refinement and validation statistics
| YicC-RNA | |
|---|---|
|
| |
| Data collection and processing | |
|
| |
| Magnification | 81,000 |
|
| |
| Voltage (kV) | 300 |
|
| |
| Electron exposure (e−/Å2) | 50 |
|
| |
| Defocus range (μm) | 0.5–2 |
|
| |
| Pixel size (Å) | 1.07 |
|
| |
| Symmetry imposed | C1 |
|
| |
| Initial particle images (no.) | 7,981,098 |
|
| |
| Final particle images (no.) | 342,211 |
|
| |
| Map resolution (Å) | 3.22 |
|
| |
| FSC threshold | 0.143 |
|
| |
| Map resolution range (Å) | 2.9–7.9 |
|
| |
| Refinement | |
|
| |
| Initial model used (PDB code) | Apo structure |
|
| |
| Model resolution (Å) | 3.22 Å |
| FSC threshold | 0.143 |
|
| |
| Map sharpening B factor (Å2) | -144.3 |
|
| |
| Model composition | |
| Non-hydrogen atoms | 14326 |
| Protein residues | 13893 |
| Nucleotides | 431 |
|
| |
| B factors (Å2) | |
| Protein | |
| Nucleotides | |
|
| |
| R.m.s. deviations | |
| Bond lengths (Å) | 0.004 |
| Bond angles (°) | 0.394 |
|
| |
| Validation | |
| MolProbity score | 1.21 (99th percentile) |
| Clashscore | 4.26 (96th percentile) |
| Poor rotamers (%) | 0% |
|
| |
| Ramachandran plot | |
| Favored (%) | 98.65% |
| Allowed (%) | 1.35% |
| Disallowed (%) | 0% |