Table 1 Cryo-EM data collection, refinement and validation statistics
From: Molecular glues that inhibit deubiquitylase activity and inflammatory signaling
BRISC∆N∆C + FX-171-C | BRISC∆N∆C + JMS-175-2 | BRISC (FL) | |
|---|---|---|---|
Data collection and processing | |||
Microscope | FEI Titan Krios G2 | ||
Detector | Thermo Fisher Scientific Falcon 4 | Thermo Fisher Scientific Falcon 4 | Thermo Fisher Scientific Falcon 4 |
Energy filter | Thermo Fisher Scientific Selectris X | Thermo Fisher Scientific Selectris X | |
Energy filter slit (eV) | 10 | 10 | |
Magnification | ×165,000 | ×96,000 | ×165,000 |
Voltage (kV) | 300 | 300 | 300 |
Spot size | 7 | 6 | 8 |
Illuminated area (µm) | 0.8 | 1 | 0.53 |
Pixel size (Å) | 0.71 | 0.82 | 0.74 |
Defocus range (µm) | −1.6 to −2.5 | −1.7 to −3.1 | −0.9 to −2.7 |
Total electron dose (e− per Å2) | 34.97 | 39.84 | 40.46 |
Exposure (s) | 3.43 | 5.99 | 2.78 |
Number of frames | 44 | 40 | 40 |
Electron dose per frame (e− per Å2) | 0.8 | 0.99 | 1 |
Videos collected | 16,750 | 7,768 | 14,573 |
Acquisition mode | Counting | Counting | Counting |
Symmetry imposed | C1 | C1 | C1, C2 |
Initial particle images (no.) | 2,458,785 | 1,616,457 | 1,933,988 |
Final particle images (no.) | 632,988 | 371,872 | 34,099 (monomer) |
32,283 (dimer) | |||
Map resolution (Å) | 3.02 | 3.32 | 7.1 (monomer) |
7.2 (dimer, C1) | |||
8.3 (dimer, C2) | |||
FSC threshold | 0.143 | 0.143 | 0.143 |
Map resolution range (Å) | 2.8–5.4 | 3.1–7.8 | 4.0–7.0 (monomer) |
4.0–7.0 (dimer, C1) | |||
5.0–9.0 (dimer, C1) | |||
Refinement | |||
Initial models used (PDB code) | |||
Model resolution (Å) | 2.7 | 3.1 | |
FSC threshold | 0.143 | 0.143 | |
Model composition | |||
Nonhydrogen atoms | 35,736 | 35,730 | |
Protein residues | 4,436 | 4,436 | |
Ligands | Zn: 4 | Zn: 4 | |
FX-171-C: 2 | JMS-175-2: 2 | ||
B factors (Å) | |||
Protein | 60.66 | 22.53 | |
Ligands | 18.46 | 11.95 | |
Root-mean-square deviation from ideal geometry | |||
Bond lengths (Å) | 0.003 | 0.002 | |
Bond angles (°) | 0.72 | 0.519 | |
Validation | |||
MolProbity score | 1.97 | 1.94 | |
Clashscore | 9.94 | 11.14 | |
Ramachandran plot | |||
Favored (%) | 92.85 | 94.47 | |
Allowed (%) | 7.15 | 5.53 | |
Disallowed (%) | 0 | 0 | |
Rotamer outliers (%) | 0.13 | 0.33 | |
Cβ outliers (%) | 0 | 0 | |
cis-proline (%) | 0 | 0 | |
CaBLAM outliers (%) | 3.95 | 3.31 | |
