Table 1 Cryo-EM data collection, refinement and validation statistics
From: Design of minibinder proteins as universal antagonists against canine and human TNFα
cTNFa-TNF30K (PDB: 9JEC, EMD-61412) | |
|---|---|
Data collection and processing | |
Magnification | 105,000 |
Voltage (kV) | 300 |
Electron exposure (e–/Å2) | 54 |
Defocus range (μm) | 1.2–2.2 |
Pixel size (Å) | 0.85 |
Symmetry imposed | C3 |
Initial particle images (no.) | 1,365,774 |
Final particle images (no.) | 543,326 |
Map resolution (Å) FSC threshold | 3.1 0.143 |
Map resolution range (Å) | 3.1–5.0 |
Refinement | |
Initial model used (PDB code) | AlphaFold2 |
Model resolution (Å) FSC threshold | 3.1 0.143 |
Model resolution range (Å) | 3.1–5.0 |
Map sharpening B factor (Å2) | −193.7 |
Model composition Non-hydrogen atoms Protein residues Ligands | 5985 771 0 |
B factors (Å2) Protein Ligand | 104.38 0 |
R.m.s. deviations Bond lengths (Å) Bond angles (°) | 0.006 0.655 |
Validation MolProbity score Clashscore Poor rotamers (%) | 1.86 7.48 0.62 |
Ramachandran plot Favored (%) Allowed (%) Disallowed (%) | 92.96 7.04 0 |
