Table 1 Cryo-EM data collection, refinement and validation statistics
From: Structural basis of the histone ubiquitination read–write mechanism of RYBP–PRC1
Data collection and processing | ||
Magnification | 105,000 | 81,000 |
Voltage (kV) | 300 | 300 |
Electron exposure (e−/Å2) | 58.6 | 54.0 |
Defocus range (μm) | 0.5–3 | 0.5–3 |
Pixel size (Å) | 0.8512 | 1.0940 |
Symmetry imposed | C1 | C1 |
Initial particle images (no.) | 6,723,019 | 12,150,042 |
Final particle images (no.) | 146,136 | 640,334 |
Map resolution (Å) | 2.91 | 3.18 |
FSC threshold | 0.143 | 0.143 |
Map resolution range (Å) | 2.0–7.0 | 2.5–7.0 |
Refinement | ||
Initial model used (PDB code) | ||
Model resolution (Å) | 2.9 (unmasked) | 3.0 (unmasked) |
FSC threshold | 0.5 | 0.5 |
Model resolution range (Å) | n/a. | n/a. |
Map sharpening B factor (Å2) | −60 | −60 |
Model composition | ||
Nonhydrogen atoms | 15,562 | 13,317 |
Residues | Protein: 1,165 Nucleotide: 306 | Protein: 872 Nucleotide: 312 |
Ligands | Zn: 8 | Zn: 1 |
B factors (Å2) | ||
Protein | 25.13 | 42.62 |
Nucleotide | 52.00 | 69.40 |
Ligand | 89.39 | 178.81 |
R.m.s. deviations | ||
Bond lengths (Å) | 0.004 | 0.005 |
Bond angles (°) | 0.598 | 0.562 |
Validation | ||
MolProbity score | 1.18 | 1.17 |
Clashscore | 2.40 | 3.48 |
Rotamer outliers (%) | 0.69 | 0.00 |
Ramachandran plot | ||
Favored (%) | 97.11 | 97.89 |
Allowed (%) | 2.98 | 2.11 |
Disallowed (%) | 0.00 | 0.00 |
