Table 1.
Cryo-EM data collection, refinement and validation statistics
| FA core (EMD-23085, PDB- 7KZP) |
FA core-ID (EMD- 23086, PDB- 7KZQ) |
FA core-UBE2T-ID (EMD-23087, PDB- 7KZR) |
FA core-UBE2T-ID-DNA (ID open state: EMD-23088, PDB-7KZS; ID intermediate state: EMD-23089, PDB-7KZT; ID closed state: EMD- 23090, PDB-7KZV) |
||||
|---|---|---|---|---|---|---|---|
| Data collection and processing | |||||||
| Magnification | 22,500 | 22,500 | 22,500 | 22,500 | |||
| Voltage (kV) | 300 | 300 | 300 | 300 | |||
| Electron exposure (e–/Å2) | 65 | 65 | 60 | 36.5 | |||
| Defocus range (μm) | 0.8-3.5 | 0.8-3.5 | 0.8-3.5 | 0.9-3.2 | |||
| Pixel size (Å) | 1.089 | 1.089 | 1.072 | 1.056 | |||
| Symmetry imposed | C1 | C1 | C1 | C1 | |||
| Initial particle images (no.) | 671,972 | 289,005 | 295,721 | 531,808 | |||
| Final particle images (no.) | 671,972 | 76,111 | 114,249 | 332,563 | 40,749 | 69,111 | 74,481 |
| Map resolution (Å) | ID+ subset | Open | Intermediate | Closed | |||
| Consensus reconstruction | 3.4 | 4.2 | 4.4 | 4.1 | 6.2 | 4.7 | 4.7 |
| Focus 1 reconstruction | 3.1 | 3.9 | 4.1 | 3.5 | 4.1 | 3.9 | 3.9 |
| Focus 2 reconstruction | 3.1 | 4.5 | 3.9 | 3.5 | 4.5 | 4.3 | 4.1 |
| Focus 3 reconstruction | 3.1 | 4.3 | 4.0 | 3.4 | 4.2 | 3.9 | 4.2 |
| Focus 4 reconstruction | 3.1 | 4.2 | 3.7 | 4.2 | 4.2 | 4.3 | |
| Focus 5 reconstruction | 3.7 | 4.2 | |||||
| Focus 6 reconstruction | 3.4 | ||||||
| Focus 7 reconstruction | 3.4 | ||||||
| FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
| Map resolution range (Å) | |||||||
| Consensus reconstruction | 3.2-9.3 | 4.0-20.6 | 4.0-20.9 | 3.5-18.5 | 4.6-23.5 | 4.1-22.9 | 4.1-21.7 |
| Focus 1 reconstruction | 3.0-3.8 | 3.7-10.0 | 4.1-13 | 3.3-5.9 | 3.9-18 | 3.8-13.4 | 3.7-12.8 |
| Focus 2 reconstruction | 3.0-4.3 | 4.5-24.4 | 3.9-10.8 | 3.3-6.5 | 4.2-20.9 | 3.8-19.2 | 3.7-16.5 |
| Focus 3 reconstruction | 3.0-5.1 | 4.0-11.7 | 4.0-17.4 | 3.2-7.7 | 4.2-21.2 | 3.9-16.2 | 4.1-17.0 |
| Focus 4 reconstruction | 3.2-6.3 | 4.1-10.3 | 3.6-20.9 | 4.2-24.9 | 4.1-24.9 | 4.3-17.9 | |
| Focus 5 reconstruction | 3.6-4.8 | 4.2-24 | |||||
| Focus 6 reconstruction | 3.3-5.3 | ||||||
| Focus 7 reconstruction | 3.3-5.7 | ||||||
| Refinement | |||||||
| Initial model used | De novo modelling/2IQC/3K1L/3ZQS | FA Core/3S4W/2ILR | FA Core/3S4W/2ILR/4CCG | FA Core/3S4W/2ILR/4CCG | |||
| Model resolution (Å) | 3.1 | 4.3 | 4.2 | - | 4.2 | 4.2 | 4.2 |
| FSC threshold | 0.55 | 0.81 | 0.55 | - | 0.74 | 0.71 | 0.67 |
| Model resolution range (Å) | 20.0-3.1 | 20.0-4.3 | 314.6-4.2 | - | 20.0-4.2 | 20.0-4.2 | 40.0-4.2 |
| Map sharpening B factor (Å2) | −(85-110) | −(68-94) | −(68-137) | - | −(91-132) | −(96-133) | −(99-145) |
| Model composition | |||||||
| Non-hydrogen atoms | 64,462 | 85,275 | 86,745 | - | 87,800 | 87,510 | 88,223 |
| Protein residues | 8,218 | 10,829 | 11,021 | - | 11,021 | 11,001 | 11,053 |
| DNA residues | - | - | - | - | 1,025 | 902 | 1,189 |
| Ligand | 3 | 5 | 5 | - | 5 | 5 | 5 |
| B factors (Å2) | |||||||
| Protein | 152 | 308 | 254 | - | 262 | 283 | 289 |
| DNA | - | - | - | - | 365 | 506 | 420 |
| Ligand | 104 | 235 | 249 | - | 211 | 236 | 242 |
| R.m.s. deviations | |||||||
| Bond lengths (Å) | 0.014 | 0.015 | 0.011 | - | 0.009 | 0.009 | 0.010 |
| Bond angles (°) | 1.623 | 1.706 | 1.400 | - | 1.867 | 1.979 | 2.092 |
| B factors main chain (Å2) | 4.1 | 4.0 | 2.8 | - | 3.184 | 3.608 | 3.543 |
| B factors side chain (Å2) | 3.7 | 3.0 | 2.0 | - | 2.326 | 2.866 | 2.658 |
| Validation | |||||||
| MolProbity score | 1.61 | 2.09 | 1.97 | - | 2.63 | 2.92 | 2.88 |
| Clashscore | 2.99 | 9.02 | 7.71 | - | 8.42 | 11.21 | 10.93 |
| Poor rotamers (%) | 0.73 | 0.33 | 0.17 | - | 6.49 | 10.18 | 8.96 |
| Ramachandran plot | |||||||
| Favored (%) | 90.81 | 87.54 | 90.22 | - | 89.61 | 88.68 | 88.15 |
| Allowed (%) | 8.61 | 12.1 | 9.48 | - | 9.42 | 10.18 | 10.46 |
| Disallowed (%) | 0.58 | 0.36 | 0.30 | - | 0.97 | 1.14 | 1.39 |
| Rwork (%) | 30.6 | 31.86 | 31.29 | - | 32.83 | 33.53 | 32.55 |
| Average FSC | 0.84 | 0.86 | 0.77 | - | 0.85 | 0.839 | 0.831 |