Table 1 Cryo-EM data collection, refinement and validation statistics
From: Mechanism of millisecond Lys48-linked poly-ubiquitin chain formation by cullin-RING ligases
Ligation mimic UBE2R2 NEDD8 CRL | Yes Yes Yes CRL2FEM1C (EMD-17803) (EMD-17822) (PDB 8PQL) | Yes Yes Yes CRL2VHL-MZ1 (EMD-18767) | Yes Yes Yes CRL1FBXW7 (EMD-17802) | No No No CRL2FEM1C Map1 Map2 | No No Yes CRL2FEM1C Map1 Map2 (Map1: EMD-17800) (Map2: EMD-17801) | ||
|---|---|---|---|---|---|---|---|
Data collection and processing | |||||||
Microscope | Krios | Krios | Glacios | Glacios | Glacios | ||
Magnification | 130,000 | 130,000 | 22,000 | 22,000 | 22,000 | ||
Voltage (kV) | 300 | 300 | 200 | 200 | 200 | ||
Electron exposure (e–/Å2) | 66 | 66 | 59 | 60 | 60 | ||
Defocus range (μm) | −0.6 ∼ −2.2 | -0.6 ∼ −2.2 | −0.6 ∼ −2.6 | −0.6 ∼ −2.6 | −0.6 ∼ −2.6 | ||
Pixel size (Å) | 0.8512 | 0.8512 | 1.885 | 1.885 | 1.885 | ||
Symmetry imposed | C1 | C1 | C1 | C1 | C1 | ||
Initial particle images (no.) | 4,187,858 | 1,210,530 | 2,989,541 | 2,801,309 | 2,963,610 | ||
Final particle images (no.) | 61,956* | 12,520 | 65,467 | 56,038 | 38,547 | 51,322 | 28,677 |
Map resolution (Å) FSC threshold | 3,76** (0,143) | 7,5 (0,143) | 8,1 (0,143) | 7,72 (0,143) | 7,54 (0,143) | 7,19 (0,143) | 6,88 (0,143) |
Map resolution range (Å) | − | − | − | − | − | − | − |
Refinement | |||||||
Initial model used (PDB code) | |||||||
Model resolution (Å) FSC threshold | 3.8 (0.143) | ||||||
Model resolution range (Å) | |||||||
Map sharpening B factor (Å2) | −70*** | −160 | −350 | −250 | −300 | −300 | −150 |
Model composition | |||||||
Non-hydrogen atoms | 13554 | ||||||
Protein residues | 1837 | ||||||
Ligands | 3(ZN) | ||||||
B factors (Å2) | |||||||
Protein | 77.63 | ||||||
Ligand | 92.01 | ||||||
R.m.s. deviations | |||||||
Bond lengths (Å) | 0.004 | ||||||
Bond angles (°) | 0.729 | ||||||
Validation | |||||||
MolProbity score | 1.96 | ||||||
Clashscore | 7.85 | ||||||
Poor rotamers (%) | 0.38 | ||||||
Ramachandran plot | |||||||
Favored (%) | 90.54 | ||||||
Allowed (%) | 9.46 | ||||||
Disallowed (%) | 0.00 | ||||||
