Table 1. Cryo-EM data collection, refinement and validation statistics.
| RFC-PCNADNA1open(EMD-27663)(PDB 8DQX) | RFC-PCNADNA1 intermediate(EMD-27666)(PDB 8DQZ) | RFC-PCNADNA1closed(EMD-27667)(PDB 8DR0) | RFC-PCNADNA2 closed consensus(EMD-27668)(PDB 8DR1) | RFC-PCNADNA2 closed with NTD(EMD-27669)(PDB 8DR3) | RFC-PCNADNA2 open no NTD(EMD-27670)(PDB 8DR4) | RFC-PCNADNA2 open with NTD(EMD-27671)(PDB 8DR5) | RFC-PCNAnicked DNA closed(EMDB-27672)(PDB 8DR6) | RFC-PCNAnicked DNA open(EMDB-27673)(PDB 8DR7) | Rad24-RFCOpen(EMD- 27662)(PDB 8DQW) | |
|---|---|---|---|---|---|---|---|---|---|---|
| Data collection and processing | ||||||||||
| Magnification | 29,000 x | 29,000 x | 29,000 x | 29,000 x | 29,000 x | 29,000 x | 29,000 x | 29,000 x | 29,000 x | 29,000 x |
| Voltage (kV) | 300 keV | 300 keV | 300 keV | 300 keV | 300 keV | 300 keV | 300 keV | 300 keV | 300 keV | 300 keV |
| Electron exposure (e–/Å2) | 66 | 66 | 66 | 66 | 66 | 66 | 66 | 66 | 66 | 66 |
| Defocus range (μm) | –0.5 to –2.0 | –0.5 to –2.0 | –0.5 to –2.0 | –0.5 to –2.0 | –0.5 to –2.0 | –0.5 to –2.0 | –0.5 to –2.0 | –0.5 to –2.0 | –0.5 to –2.0 | –0.5 to –2.0 |
| Pixel size (Å) | 0.826 | 0.826 | 0.826 | 0.826 | 0.826 | 0.826 | 0.826 | 0.826 | 0.826 | 0.826 |
| Symmetry imposed | C1 | C1 | C1 | C1 | C1 | C1 | C1 | C1 | C1 | C1 |
| Initial particle images (no.) | 5,688,448 | 5,688,448 | 5,688,448 | 3,356,580 | 3,356,580 | 3,356,580 | 3,356,580 | 2,031,079 | 2,031,079 | 4,117,022 |
| Final particle images (no.) | 616,330 | 41,190 | 252,647 | 872,447 | 356,424 | 104,742 | 61,483 | 359,126 | 142,294 | 938,420 |
| Map resolution (Å) | 2.1 | 2.92 | 2.42 | 2.14 | 2.2 | 2.45 | 2.76 | 2.39 | 2.7 | 2.1 |
| FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
| Refinement | ||||||||||
| Initial model used (PDB code) | Closed state | Open state | 1SXJ | Closed state | Closed state | Open state | Open state | Closed state | Open state | 7ST9 |
| Model resolution (Å) | 1.99 | 2.87 | 2.25 | 2.05 | 2.13 | 2.3 | 2.69 | 2.3 | 2.66 | 2.12 |
| FSC threshold | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 |
| Model composition | ||||||||||
| Non-hydrogen atoms | 22,030 | 21,451 | 21,514 | 22,004 | 23,129 | 21,999 | 22,780 | 217,998 | 21,655 | 23,629 |
| Protein residues | 2,598 | 2,599 | 2,608 | 2,609 | 2,758 | 2,608 | 2,749 | 2,608 | 2,600 | 2,802 |
| Nucleotide residues | 26 | 40 | 40 | 63 | 63 | 63 | 49 | 63 | 49 | 35 |
| Ligands | 9 | 9 | 9 | 9 | 9 | 9 | 9 | 9 | 9 | 9 |
| B factors (Å2) | ||||||||||
| Protein (mean) | 10 | 75.3 | 34.7 | 10.8 | 21.5 | 50.6 | 42.5 | 50.6 | 33.9 | 9.8 |
| Nucleotide (mean) | 6.7 | 161.8 | 85 | 25.5 | 52.6 | 97.2 | 83 | 97.2 | 80.7 | 41.9 |
| Ligand (mean) | 3.2 | 56.9 | 25.2 | 5 | 11.3 | 38 | 22.9 | 39.3 | 15.5 | 7.4 |
| R.m.s. deviations | ||||||||||
| Bond lengths (Å) | 0.004 | 0.002 | 0.002 | 0.003 | 0.002 | 0.002 | 0.002 | 0.002 | 0.002 | 0.002 |
| Bond angles (°) | 0.628 | 0.515 | 0.475 | 0.528 | 0.476 | 0.479 | 0.5 | 0.479 | 0.528 | 0.479 |
| Validation | ||||||||||
| MolProbity score | 1.31 | 1.3 | 1.17 | 1.12 | 1.19 | 1.12 | 1.29 | 1.12 | 1.28 | 1.15 |
| Clashscore | 5.05 | 5.53 | 3.68 | 3.25 | 3.22 | 3.25 | 4.82 | 3.25 | 5.17 | 3.61 |
| Poor rotamers (%) | 1.13 | 0.26 | 1.04 | 0.65 | 1.28 | 0 | 0.45 | 0.87 | 0.82 | 0.4 |
| Ramachandran plot | ||||||||||
| Favored (%) | 98.06 | 98.06 | 98.65 | 98.65 | 98.43 | 98.61 | 97.84 | 98.61 | 98.1 | 98.48 |
| Allowed (%) | 1.94 | 1.94 | 1.35 | 1.35 | 1.57 | 1.39 | 2.16 | 1.39 | 1.9 | 1.52 |
| Disallowed (%) | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |