Extended Data Table 2. NCP cryo-EM data collection, refinement and validation statistics.
| NCP6-4PP (EMD-4767) (PDB 6R93) |
NCPTHF2(-3) (EMD-4768) (PDB 6R94) |
|
|---|---|---|
| Data collection and processing | ||
| Magnification | 130,000 | 130,000 |
| Voltage (kV) | 300 | 300 |
| Electron exposure (e–/Å2) | 40 | 40 |
| Defocus range (µm) | -0.4 – -0.7 | -1.0 – -3.0 |
| Pixel size (Å) | 0.86 | 0.86 |
| Symmetry imposed | C1 | C1 |
| Initial particle images (no.) | 827,045 | 266,180 |
| Final particle images (no.) | 98,387 | 78,672 |
| Map resolution (Å) | 4.0 | 3.5 |
| FSC threshold | 0.143 | 0.143 |
| Map resolution range (Å) | 3.1–12 | 3.0–12 |
| Refinement | ||
| Initial models used (PDB codes) | 4ZUX, 5Y0C | 4ZUX, 5Y0C |
| Model resolution (Å) | 3.8 | 3.4 |
| FSC threshold | 0.143 | 0.143 |
| Map sharpening B factor (Å2) | -110 | -140 |
| Model composition | ||
| Non-hydrogen atoms | 12,844 | 12,372 |
| Protein residues | 775 | 803 |
| Nucleotides | 290 | 290 |
| B factors (Å2) | ||
| Protein | 63 | 68 |
| DNA | 99 | 111 |
| DNA damage | 103 | 118 |
| R.m.s. deviations | ||
| Bond lengths (Å) | 0.008 | 0.008 |
| Bond angles (°) | 1.238 | 1.012 |
| Validation | ||
| MolProbity score | 1.15 | 1.15 |
| Clashscore | 2.04 | 1.07 |
| Poor rotamers (%) | 0.00 | 0.00 |
| Ramachandran plot | ||
| Favored (%) | 97.0 | 97 |
| Allowed (%) | 2.5 | 3.0 |
| Disallowed (%) | 0.5 | 0.4 |
| Model-to-data fit* | ||
| CCmask | 0.67 | 0.69 |
| CCbox | 0.73 | 0.74 |
| CCpeaks | 0.62 | 0.66 |
| CCvolume | 0.66 | 0.70 |