Table 2 Cryo-EM data collection, refinement, and validation statistics
From: Structure and mechanism of the two-component α-helical pore-forming toxin YaxAB
YaxAB (20-mer) (EMDB-3885) (PDB-6EL1) | |
|---|---|
Data collection and processing | |
Magnification | 59,000 |
Voltage (kV) | 300 |
Electron exposure (e–/Å2) | 60 |
Defocus range (μm) | 1.1–2.5 |
Pixel size (Å) | 1.106 |
Symmetry imposed | C10 |
Initial particle images (no.) | 178,149 |
Final particle images (no.) | 24,822 |
Map resolution (Å) | 6.1 |
FSC threshold | 0.143 |
Map resolution range (Å) | 4.8–7.0 |
Refinement | |
Initial model used (PDB code) | 6EK7, 6EK8 |
Model resolution (Å) | 6.1 |
FSC threshold | 0.143 |
Model resolution range (Å) | 4.8–7.0 |
Map sharpening B-factor (Å2) | −331 |
Model composition | |
Protein residues | 6830 |
B-factors (Å2) | |
Protein | 322 |
R.m.s. deviations | |
Bond lengths (Å) | 0.005 |
Bond angles (°) | 0.93 |
Validation | |
MolProbity score | 1.87 |
Clashscore | 7.4 |
Poor rotamers (%) | 0.5 |
Ramachandran plot | |
Favored (%) | 92.5 |
Allowed (%) | 7.5 |
Disallowed (%) | 0 |
