Table 1 Data collection and refinement statistics for cryo-EM datasets
From: Unveiling the hidden interactome of CRBN molecular glues
CRBN-DDB1 FPFT-2216 PPIL4 RRM | CRBN-DDB1∆B FPFT-2216-PDE6D Consensus refine | CRBN-DDB1∆B FPFT-2216-PDE6D Local refine | |
|---|---|---|---|
Microscope | Talos Arctica | Talos Arctica | |
Voltage (kV) | 200 | 200 | |
Camera | Gatan K3 | Gatan K3 | |
Magnification (X) | 36,000 | 36,000 | |
Pixel size (Å) | 1.1 | 1.1 | |
Total electron exposure (e−/Å2) | 54 | 51.2 | |
Number of frames | 40 | 50 | |
Defocus range (μm) | − 2.0 to − 0.8 | − 2.0 to − 0.8 | |
Data collection software | SerialEM4.1b | ||
Micrographs collected | 4170 | 4474 | |
Total extracted particles | 3,198,055 | 3,393,589 | |
EMDB accession code | EMD-47268 | EMD-47269 | EMD-47270 |
PDB accession code | PDB-9DWV | PDB-9DWW | |
Final particles used | 219,802 | 515,636 | 515,636 |
Map resolution (Å, FSC 0.143) | 3.5 | 3.3 | 3.4 |
FSC threshold | 0.143 | 0.143 | 0.143 |
Model composition | |||
Protein residues | 1211 | 1260 | |
Ligands | 2 | 2 | |
Refinement package | phenix.real_space_refine | ||
Model-to-map CC | 0.72 | 0.78 | |
Model-to-map FSC (Å, FSC 0.5) | 3.8 | 3.5 | |
Mean B factors (Å2) | |||
Protein | 63.69 | 98.29 | |
Ligand | 69.37 | 118.85 | |
Bond root-mean-square deviation (RMSD) | |||
Lengths (Å) | 0.005 | 0.005 | |
Angles (°) | 0.615 | 0.797 | |
Validation | |||
MolProbity score | 2.05 | 1.53 | |
Clash score | 11.78 | 6.37 | |
Rotamer outliers (%) | 1.27 | 0.11 | |
CaBLAM outliers (%) | 2.76 | 1.54 | |
Ramachandran plot | |||
Favored (%) | 94.26 | 96.96 | |
Allowed (%) | 5.74 | 3.04 | |
Disallowed (%) | 0.00 | 0.00 | |
