Table 1 Data collection, refinement and validation statistics
From: TRIP12 structures reveal HECT E3 formation of K29 linkages and branched ubiquitin chains
Full-length TRIP12, K29/K48 branched chain formation complex (EMDB-51428) | TRIP12ΔN, K29/K48 branched chain formation complex (screening dataset) | TRIP12ΔN, K29/K48 branched chain formation complex (EMDB-51429) (PDB 9GKM) | TRIP12ΔN, K29 chain formation complex (screening dataset) | TRIP12ΔN, K29 chain formation complex (EMDB-51430) (PDB 9GKN) | |
|---|---|---|---|---|---|
Data collection and processing | |||||
Magnification | ×105,000 | ×22,000 | ×105,000 | ×22,000 | ×105,000 |
Voltage (kV) | 300 | 200 | 300 | 200 | 300 |
Electron exposure (e– per Å2) | 76.5 | 60.0 | 64.8 | 60.0 | 66.8 |
Defocus range (μm) | –0.6 to –2.2 | –0.8 to –2.6 | –0.6 to –2.2 | –0.8 to –2.6 | –0.6 to –2.2 |
Pixel size (Å) | 0.8512 | 1.841 | 0.8512 | 1.841 | 0.8512 |
Symmetry imposed | C1 | C1 | C1 | C1 | C1 |
Initial particle images (no.) | 6,505,263 | 1,319,552 | 939,881 | 1,871,755 | 5,689,483 |
Final particle images (no.) | 891,840 | 573,040 | 122,281 | 358,901 | 427,215 |
Map resolution (Å) | 3.2 | 4.3 | 3.7 | 6.9 | 3.4 |
Fourier shell correlation threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
Map resolution range (Å) | 1.8–49.1 | 4.1–12.3 | 3.1–14.4 | 5.1–61.0 | 1.8–15.1 |
Refinement | |||||
Initial model used (PDB code) | AlphaFold 2 multimer | AlphaFold 2 multimer | |||
Model resolution (Å) | 3.7 | 3.4 | |||
Fourier shell correlation threshold | 0.143 | 0.143 | |||
Model resolution range (Å) | 3.1–14.4 | 1.8–15.1 | |||
Map sharpening B factor (Å2) | – | – | |||
Model-map correlation (box) | 0.74 | 0.76 | |||
Model composition | |||||
Non-hydrogen atoms | 11,231 | 10,763 | |||
Protein residues | 1446 | 1384 | |||
Ligands | 1 (SY8) | 1 (SY8) | |||
B factors (Å2) | |||||
Protein | 77.5 | 74.2 | |||
Ligand | 81.3 | 62 | |||
Root mean square deviations | |||||
Bond lengths (Å) | 0.002 | 0.003 | |||
Bond angles (°) | 0.497 | 0.548 | |||
Validation | |||||
MolProbity score | 1.71 | 1.63 | |||
Clashscore | 6.29 | 4.85 | |||
Poor rotamers (%) | 0 | 0 | |||
Ramachandran plot | |||||
Favored (%) | 94.7 | 94.55 | |||
Allowed (%) | 5.3 | 5.45 | |||
Disallowed (%) | 0 | 0 | |||
