Extended Data Table 1.
Cryo-EM data collection, model refinement and validation statistics.
| Partially-homologous 67 bp dsDNA | Non-homologous 120 bp dsDNA | D-loopDG | D-loopDH | |
|---|---|---|---|---|
| (PDB-7JY6) | (PDB-7JY8) | (PDB-7JY9) | (PDB-7JY7) | |
| (EMDB-22522) | (EMDB-22524) | (EMDB-22525) | (EMDB-22523) | |
|
| ||||
| Data collection and processing | ||||
| Magnification | 81,000 | 81,000 | 105,000 | 105,000 |
| Voltage (kV) | 300 | 300 | 300 | 300 |
| Electron exposure (e-/Å2) | 51.6 | 53.7 | 56.6 | 66.6 |
| Defocus range (urn) | 1.0–2.5 | 0.8–2.5 | 1.0–2.5 | 1.0–2.5 |
| Pixel size (Å) | 1.078 | 1.078 | 1.096 | 1.096 |
| Symmetry imposed | Cl | Cl | Cl | Cl |
| Initial particle images (no.) | 1,697,726 | 1,592,037 | 399,184 | 222,426 |
| Final particle images (no.) | 1,697,726 | 1,592,037 | 399,184 | 222,426 |
| Map resolution (Å) | ||||
| Consensus reconstruction | 2.4 | 2.5 | 2.7 | 2.9 |
| Focus ABCD reconstruction | 2.4 | 2.4 | 2.8 | 2.9 |
| Focus FGHI reconstruction | 2.4 | 2.4 | 2.6 | 2.9 |
| FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 |
| Map resolution range (Å) | ||||
| Consensus reconstruction | 2.3–4.1 | 2.3–6.9 | 2.6–6.9 | 2.1–12 |
| Focus ABCD reconstruction | 2.3–3.7 | 2.3–4.2 | 2.6–6.5 | 2.1–63 |
| Focus FGHI reconstruction | 2.4–3.5 | 2.3–3.9 | 2.7–4.8 | 2.1–63 |
| Refinement | ||||
| Initial model used (PDB code) | 3CMW | 3CMW | 3CMX | 3CMX |
| Model resolution (Å) | 2.5 | 2.5 | 2.8 | 2.9 |
| FSC threshold | 0.70 | 0.68 | 0.71 | 0.68 |
| Model resolution range (Å) | 195–2.5 | 195–2.5 | 197–2.8 | 196–2.9 |
| Map sharpening B factor (Å2) | −73 | −71 | −71 | −64 |
| Model composition | ||||
| Non-hydrogen atoms | 23,389 | 24,059 | 24,858 | 25,127 |
| Protein residues | 2,967 | 2,967 | 2,964 | 2,967 |
| DNA residues | 38 | 72 | 111 | 123 |
| Cofactors | 9 | 9 | 9 | 9 |
| B factors (Å2) | ||||
| Protein | 78.0 | 92.9 | 75.8 | 111.1 |
| DNA | 89.0 | 185.7 | 151.7 | 222.7 |
| Cofactors | 41.5 | 47.8 | 29.6 | 65.6 |
| R.m.s. deviations | ||||
| Bond lengths (Å) | 0.006 | 0.006 | 0.006 | 0.006 |
| Bond angles (°) | 1.57 | 1.55 | 1.52 | 1.53 |
| B factors main chain (Å2) | 3.37 | 3.73 | 2.47 | 2.54 |
| B factors side chain (Å2) | 3.49 | 4.77 | 2.58 | 2.83 |
| Validation | ||||
| MolProbity score | 1.68 | 1.62 | 1.54 | 1.75 |
| Clashscore | 1.06 | 0.93 | 0.75 | 1.0 |
| Poor rotamers (%) | 7.58 | 5.40 | 5.70 | 7.84 |
| Ramachandran plot | ||||
| Favored (%) | 96.71 | 95.96 | 96.54 | 96.03 |
| Allowed (%) | 3.29 | 3.70 | 3.12 | 3.56 |
| Disallowed (%) | 0.17 | 0.34 | 0.34 | 0.41 |
| Rwork (%) | 27.60 | 28.89 | 26.60 | 26.75 |
| Average FSC | 0.89 | 0.89 | 0.90 | 0.89 |