Extended Data Table 1 |.
Cryo-EM data collection, refinement, and validation statistics.
| Apo monomer (EMDB-29033) (PDB 8FEX) | RNA/DNA bound monomer (map1) (EMDB-40679) (PDB N/A) | RNA/DNA bound monomer (EMDB-40670) (PDB 8SQU) | Symmetric dimer (EMDB-40672) (PDB 8SP0) | Asymmetric dimer (EMDB-40673) (PDB 8SP3) | Tetramer (EMDB-29043) (PDB 8FFI) | Tetramer with NAD+ (EMDB-40680) (PDB 8SPO) | |
|---|---|---|---|---|---|---|---|
|
| |||||||
| Data collection and processing | |||||||
| Magnification | 81,000 | 81,000 | 81,000 | 81,000 | 81,000 | 81,000 | 81,000 |
| Voltage (kV) | 300 | 300 | 300 | 300 | 300 | 300 | 300 |
| Electron exposure (e–/Å2) | 50 | 50 | 50 | 50 | 50 | 50 | 50 |
| Defocus range (μm) | 1.0 – 2.5 | 0.5 – 2.0 | 0.5 – 2.1 | 0.5 – 2.1 | 0.5 – 2.1 | 0.5 – 2.1 | 0.5 – 2.0 |
| Pixel size (Å) | 1.0694 | 0.95 | 0.95 | 0.95 | 0.95 | 0.95 | 0.899 |
| Symmetry imposed | C1 | C1 | C1 | C1 | C1 | C1 | C1 |
| Initial images (no.) | 3,464 | 6,566 | 4,823 | 4,823 | 4,823 | 4,823 | 4,215 |
| Initial particle images (no.) | 9,423,011 | 10,736,069 | 2,941,885 | 2,941,885 | 2,941,885 | 2,941,885 | 2,209,672 |
| Final particle images (no.) | 217,571 | 534,729 | 163,800 | 63,761 | 32,366 | 490,999 | 847,718 |
| Map resolution (Å) | 3.07 | 3.04 | 3.28 | 3.33 | 3.52 | 2.70 | 2.98 |
| FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
| Map resolution range (Å) | 3.07 – 4.5 | 3.04 – 6.0 | 3.28 – 6.0 | 3.33 – 6.0 | 3.52 – 6.0 | 2.51 – 4.5 | 2.98 – 6.5 |
| Refinement | |||||||
| Initial model used (PDB code) | AlphaFold | N/A | AlphaFold | AlphaFold | AlphaFold | AlphaFold | AlphaFold |
| Model resolution (Å) | 3.2 | N/A | 3.8 | 3.8 | 4.1 | 2.9 | 3.7 |
| FSC threshold | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 | |
| Map sharpening B factor (Å2) | -115.5 | -178.6 | -170.1 | -107.8 | -95.7 | -95.9, -97.7, -73.6, -95.0, -99.1 | -55.3 |
| Model composition | |||||||
| Non-hydrogen atoms | 7302 | N/A | 7768 | 16270 | 16270 | 32540 | 32628 |
| Protein residues | 891 | 842 | 1776 | 1776 | 3552 | 3552 | |
| Ligands | 0 | MG: 1 | MG: 2 | MG: 2 | MG: 4 | MG: 4 NAD+: 2 |
|
| Nucleotide | 0 | 41 | 82 | 82 | 164 | 164 | |
| B factors (Å2) | N/A | ||||||
| Protein | 63.65 | 44.11 | 45.04 | 44.84 | 49.19 | 49.19 | |
| Ligand | 30.86 | 26.92 | 26.92 | 27.07 | 38.10 | ||
| Nucleotide | 61.31 | 60.06 | 60.06 | 62.11 | 62.11 | ||
| R.m.s. deviations | N/A | ||||||
| Bond lengths (Å) | 0.004 | 0.006 | 0.005 | 0.004 | 0.004 | 0.004 | |
| Bond angles (°) | 0.910 | 1.016 | 1.024 | 0.965 | 0.918 | 0.991 | |
| Validation | N/A | ||||||
| MolProbity score | 1.80 | 1.77 | 1.70 | 1.73 | 1.59 | 1.98 | |
| Clashscore | 7.41 | 6.95 | 5.71 | 6.06 | 3.83 | 10.59 | |
| Poor rotamers (%) | 0.00 | 0.40 | 0.38 | 0.31 | 0.00 | 0.35 | |
| Ramachandran plot | N/A | ||||||
| Favored (%) | 94.24 | 94.34 | 94.27 | 94.16 | 93.57 | 93.34 | |
| Allowed (%) | 5.76 | 5.42 | 5.50 | 5.73 | 6.26 | 6.29 | |
| Disallowed (%) | 0.00 | 0.24 | 0.23 | 0.11 | 0.17 | 0.37 | |