Extended Data Table 1. NCP-UV-DDB complex cryo-EM data collection, refinement and validation statistics.
| NCP6-4PP-UV-DDB (EMD-4762) (PDB 6R8Y) |
NCPTHF2(-1)-UV-DDB (EMD-4763) (PDB 6R8Z) |
NCPTHF2(-3)-UV-DDB (EMD-4765) (PDB 6R91) |
NCPTHF2(+1)-UV-DDB class A (EMD-4764) (PDB 6R90) |
NCPTHF2(+1)-UV-DDB class B (EMD-4766) (PDB 6R92) |
|
|---|---|---|---|---|---|
| Data collection and processing | |||||
| Magnification | 130,000 | 105,000 | 130,000 | 130,000 | 130,000 |
| Voltage (kV) | 300 | 300 | 300 | 300 | 300 |
| Electron exposure (e−/Å2) | 40 | 60 | 40 | 40 | 40 |
| Defocus range (µm) | -0.4 – -0.7 | -1.0 – -3.0 | -0.4 – -0.7 | -0.4 – -0.7 | -0.4 – -0.7 |
| Pixel size (Å) | 0.86 | 0.55 (super resolution) | 1.72 (data 2 x binned) | 0.86 | 0.86 |
| Symmetry imposed | C1 | C1 | C1 | C1 | C1 |
| Initial particle images (no.) | 1,355,846 | 511,505 | 719,698 | 1,078,133 | 1,078,133 |
| Final particle images (no.) | 84,000 | 129,986 | 119,309 | 128,763 | 48,925 |
| Map resolution (Å) | 4.3 | 3.9 | 4.2 | 4.5 | 4.8 |
| FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
| Map resolution range (Å) | 3.0−12 | 3.0−12 | 4.0−7 | 4.0−12 | 4.0−12 |
| Refinement | |||||
| Initial models used (PDB codes) | 4ZUX, 5Y0C, 4E54, 3EI4 | 4ZUX, 5Y0C, 4E54, 3EI4 | 4ZUX, 5Y0C, 4E54, 3EI4 | 4ZUX, 5Y0C, 4E54, 3EI4 | 4ZUX, 5Y0C, 4E54, 3EI4 |
| Model resolution (Å) | 3.9 | 3.8 | 4.4 | 4.2 | 4.5 |
| FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
| Map sharpening B factor (Å2) | -120 | -233 | -180 | -160 | -200 |
| Model composition | |||||
| Non-hydrogen atoms | 21,717 | 21,617 | 21,477 | 21,268 | 21,500 |
| Protein residues | 1996 | 1984 | 1969 | 1944 | 1974 |
| Nucleotides | 288 | 288 | 288 | 288 | 288 |
| B factors (Å2) | |||||
| Protein | 85 | 118 | 257 | 156 | 261 |
| DNA | 73 | 90 | 264 | 155 | 244 |
| DNA damage | 64 | 74 | 229 | 143 | 249 |
| R.m.s. deviations | |||||
| Bond lengths (Å) | 0.012 | 0.009 | 0.005 | 0.005 | 0.007 |
| Bond angles (°) | 1.301 | 0.932 | 0.944 | 0.873 | 1.107 |
| Validation | |||||
| MolProbity score | 1.44 | 1.48 | 1.43 | 1.41 | 1.58 |
| Clashscore | 2.71 | 1.98 | 2.15 | 2.00 | 4.28 |
| Poor rotamers (%) | 0.47 | 0.18 | 0.65 | 0.24 | 0.36 |
| Ramachandran plot | |||||
| Favored (%) | 94.0 | 95.0 | 95.0 | 96.6 | 94.7 |
| Allowed (%) | 5.7 | 4.6 | 4.6 | 3.1 | 5.0 |
| Disallowed (%) | 0.3 | 0.4 | 0.5 | 0.3 | 0.4 |
| Model-to-data fit* | |||||
| CCmask | 0.76 | 0.75 | 0.52 | 0.72 | 0.70 |
| CCbox | 0.78 | 0.79 | 0.64 | 0.76 | 0.83 |
| CCpeaks | 0.68 | 0.71 | 0.47 | 0.61 | 0.60 |
| CCvolume | 0.74 | 0.74 | 0.53 | 0.71 | 0.71 |