Table 1.
Cryo-EM data collection, refinement and validation statistics
| 12I + 23I (EMD-7849, PDB 6DBT) |
12I + 23I (EMD-7850, PDB 6DBU) |
12I + 23I (EMD-7851, PDB 6DBV) |
12I + 23I (EMD-7847, PDB 6DBQ) |
12I + 23I (EMD-7848, PDB 6DBR) |
12I + 23I (EMD-7845, PDB 6DBL) |
12I + 23I (EMD-7846, PDB 6DBO) |
12I (EMD-7853, PDB 6DBX) |
12I (EMD-7852, PDB 6DBW) |
12N + 23N (EMD-7843, PDB 6DBI) |
12N + 23N (EMD-7844, PDB 6DBJ) |
|
|---|---|---|---|---|---|---|---|---|---|---|---|
| DNA states | Doubly unmelted |
Doubly unmelted |
12-RSS melted 23-RSS unmelted |
12-RSS unmelted 23-RSS melted |
One RSS melted The other unmelted |
Doubly melted | Doubly melted | Singly unmelted | Singly melted | Doubly nicked | Doubly nicked |
| Data collection & processing | |||||||||||
| Microscope | Titan Krios | Titan Krios | Titan Krios & Polara combined |
Titan Krios & Polara combined |
Titan Krios & Polara combined |
Titan Krios & Polara combined |
Titan Krios & Polara combined |
Titan Krios & Polara combined |
Titan Krios & Polara combined |
Titan Krios | Titan Krios |
| Magnification | 130,000 | 130,000 | 13,000/31,000 | 13,000/31,000 | 13,000/31,000 | 13,000/31,000 | 13,000/31,000 | 13,000/31,000 | 13,000/31,000 | 130,000 | 130,000 |
| Voltage (kV) | 300 | 300 | 300 | 300 | 300 | 300 | 300 | 300 | 300 | 300 | 300 |
| Electron exposure (e–/Å2) | 71.49 | 71.49 | 71.49/47 | 71.49/47 | 71.49/47 | 71.49/47 | 71.49/47 | 71.49/47 | 71.49/47 | 40 | 40 |
| Defocus range (μm) | 0.7 – 2.0 | 0.7 – 2.0 | 0.7 – 2.0/ 1.2 – 3.0 |
0.7 – 2.0/ 1.2 – 3.0 |
0.7 – 2.0/ 1.2 – 3.0 |
0.7 – 2.0/ 1.2 – 3.0 |
0.7 – 2.0/ 1.2 – 3.0 |
0.7 – 2.0/ 1.2 – 3.0 |
0.7 – 2.0/ 1.2 – 3.0 |
1.2 – 2.5 | 1.2 – 2.5 |
| Pixel size (Å) | 1.08 | 1.08 | 1.23 | 1.23 | 1.23 | 1.23 | 1.23 | 1.23 | 1.23 | 1.064 | 1.064 |
| Symmetry imposed | C1 | C2 | C1 | C1 | C1 | C1 | C2 | C1 | C1 | C1 | C2 |
| Initial particle images (no.) | 249,279 | 249,279 | 934,894 | 934,894 | 934,894 | 934,894 | 934,894 | 934,894 | 934,894 | 364,274 | 364,274 |
| Final particle images (no.) | 67,194 | 67,194 | 45,159 | 48,002 | 69,753 | 23,176 | 19,344 | 62,942 | 48851 | 53,109 | 196,652 |
| Map resolution (Å) | 4.3 | 3.9 | 4.3 | 4.2 | 4.0 | 5.0 | 4.4 | 4.2 | 4.7 | 3.4 | 3.0 |
| FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
| Map resolution range (Å) | 4.1 – 8.6 | 3.9 – 7.3 | 4.1 – 7.7 | 4.1 – 7.7 | 3.9 – 7.0 | 4.6 – 9.3 | 4.3 – 7.0 | 4.0 – 7.4 | 4.3 – 8.5 | 3.3 – 8.7 | 2.9 – 5.8 |
| Refinement | |||||||||||
| Initial model used | PDB 3JBW | PDB 3JBY | PDB 3JBW | PDB 3JBW | PDB 3JBY | PDB 3JBW | PDB 3JBY | PDB 3JBW | PDB 3JBW | PDB 3JBW | PDB 3JBY |
| Model resolution (Å) | 4.4 | 4.2 | 4.6 | 4.5 | 4.3 | 5.1 | 4.7 | 4.5 | 5.0 | 3.4 | 3.1 |
| FSC threshold | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 |
| Model resolution range (Å) | 271.4 – 4.3 (4.454 – 4.3) |
271.4 – 3.9 (4.04 – 3.9) |
237.7 – 4.3 (4.445 – 4.292) |
237.7 – 4.2 (4.371 – 4.22) |
237.7 – 4.0 (4.143 – 4.0) |
237.7 – 5.0 (5.18 – 5.001) |
237.7 – 4.4 (4.609 – 4.45) |
271.4 – 4.2 (4.35 – 4.2) |
271.4 – 4.7 (4.868 – 4.7) |
272.4 – 3.4 (3.48 – 3.36) |
192.6 – 3.0 (3.097 – 2.99) |
| Map sharpening B factor (Å2) | −173.826271 | −190.937951 | −173.907798 | −180.056215 | −179.136839 | −160.678788 | −171.589046 | −173.792903 | −195.922158 | −91.510887 | −113.457233 |
| Model composition | |||||||||||
| Nonhydrogen atoms | 19,896 | 17,010 | 19,956 | 19,956 | 17,040 | 19,929 | 16,820 | 17,436 | 17,418 | 20,001 | 16,912 |
| Protein residues | 2,152 | 1,924 | 2,161 | 2,161 | 1,930 | 2,156 | 1,914 | 2,033 | 2,031 | 2,168 | 1,932 |
| Ligands (nucleotides) | 222 | 136 | 222 | 222 | 136 | 222 | 128 | 100 | 100 | 222 | 124 |
| B factors (Å2) | |||||||||||
| Protein | 136.25 | 84.52 | 102.96 | 133.83 | 102.66 | 237.04 | 163.44 | 126.09 | 168.92 | 89.38 | 73.93 |
| Ligand (DNA) | 172.79 | 83.67 | 129.31 | 220.07 | 91.56 | 225.11 | 204.95 | 158.71 | 228.40 | 48.08 | 58.08 |
| R.m.s. deviations | |||||||||||
| Bond lengths (Å) | 0.005 | 0.007 | 0.006 | 0.005 | 0.005 | 0.016 | 0.009 | 0.005 | 0.010 | 0.010 | 0.004 |
| Bond angles (°) | 0.806 | 1.197 | 0.842 | 1.058 | 1.161 | 2.213 | 1.345 | 0.837 | 1.484 | 1.506 | 0.794 |
| Validation | |||||||||||
| MolProbity score | 2.36 | 2.37 | 2.42 | 2.49 | 2.27 | 2.48 | 2.35 | 2.4 | 2.47 | 2.05 | 2.11 |
| Clashscore | 21.46 | 22.52 | 22.61 | 27.67 | 19.39 | 37.52 | 24.81 | 20.07 | 30.04 | 15.25 | 12.23 |
| Poor rotamers (%) | 0.18 | 0.19 | 0.18 | 0.18 | 0.51 | 0.18 | 0.13 | 0.24 | 0.53 | 0.82 | 1.7 |
| Ramachandran plot | |||||||||||
| Favored (%) | 90.62 | 90.93 | 89.06 | 89.53 | 92.04 | 93.50 | 92.45 | 87.98 | 91.35 | 94.79 | 95.17 |
| Allowed (%) | 9.17 | 8.84 | 10.78 | 10.37 | 7.85 | 5.67 | 6.82 | 11.86 | 8.60 | 5.11 | 4.83 |
| Disallowed (%) | 0.21 | 0.23 | 0.16 | 0.1 | 0.11 | 0.83 | 0.73 | 0.16 | 0.05 | 0.10 | 0.00 |
*
I: intact DNA; N: nicked DNA