Table 1 Cryo-EM data collection, refinement, and validation statistics
From: Modularity of Zorya defense systems during phage inhibition
Shewanella sp. ANA-3 type I ZorAB (EMD-43563) (PDB 8VVN) | S. kujiense type II ZorAB (EMD-43560) (PDB 8VVI) | |
|---|---|---|
Data collection and processing | ||
Magnification | 165,000 | 165,000 |
Voltage (kV) | 300 | 300 |
Electron exposure (e–/Å2) | 54.0 | 57.0 |
Defocus range (μm) | −2.0 to −0.5 | −2.0 to −0.5 |
Pixel size (Å) | 0.723 | 0.723 |
Symmetry imposed | C1 | C1 |
Initial particle images (no.) | 3,905,997 | 2,729,107 |
Final particle images (no.) | 587,313 | 366,883 |
Map resolution (Å) | 2.2, 2.4 | 2.8 |
FSC threshold | 0.143 | 0.143 |
Map resolution range (Å) | 2.2–5.4 2.4–3.4 | 2.7–9.7 |
Refinement | ||
Initial model used (PDB code) | None | None |
Model resolution (Å) | 2.4 | 2.9 |
FSC threshold | 0.5 | 0.5 |
Map sharpening B factor (Å2) | −55.3, −70.3 | −85.7 |
Model composition | ||
Non-hydrogen atoms | 12938 | 7762 |
Protein residues | 1610 | 968 |
Ligands | Na: 2 | – |
B factors (Å2) | ||
Protein | 55.0 | 43.2 |
Ligand | 22.0 | – |
R.m.s. deviations | ||
Bond lengths (Å) | 0.004 | 0.002 |
Bond angles (°) | 0.600 | 0.445 |
Validation | ||
MolProbity score | 1.71 | 1.66 |
Clashscore | 9.89 | 7.21 |
Poor rotamers (%) | 0.00 | 0.00 |
Ramachandran plot | ||
Favored (%) | 96.9 | 96.1 |
Allowed (%) | 3.1 | 3.9 |
Disallowed (%) | 0 | 0 |
CC (mask) | 0.82 | 0.80 |
