Table 2 Cryo-EM data collection and refinement statistics
From: Structural insights into the substrate binding mechanism of the class I dehydratase MadB
apoMadB (EMDB-50910) (PDB 9G04) | MadB_MadL3 (EMDB-50911) (PDB 9G05) | |
|---|---|---|
Data collection and processing | ||
Magnification | 100,000x | 100,000x |
Voltage (kV) | 200 | 200 |
Electron exposure (e–/Å2) | 0.75 | 1.01 |
Defocus range (μm) | 0.5–2.5 | 0.5–3 |
Pixel size (Å) | 0.8389 | 0.8389 |
Symmetry imposed | C2 | C2 |
Initial particle images (no.) | 2,667,864 | 2,971,174 |
Final particle images (no.) | 800,314 | 994,872 |
Map resolution (Å) | 2.7 | 3.13 |
FSC threshold | 0.143 | 0.143 |
Map resolution range (Å) | 2.3–3.95 | 2.4–4.5 |
Refinement | ||
Initial model used (PDB code) | – | – |
Model resolution (Å) | 2.9 | 3.2 |
FSC threshold | 0.5 | 0.5 |
Model resolution range (Å) | 2.3–3.95 | 2.4–4.5 |
Model composition | ||
Non-hydrogen atoms | 34,114 | 34981 |
Protein residues | 2047 | 2100 |
Ligands | 2 | |
B factors (Å2) | ||
Protein | 54.61 | 40.30 |
Ligand | ||
R.m.s. deviations | ||
Bond lengths (Å) | 0.005 | 0.005 |
Bond angles (°) | 0.773 | 0.580 |
Validation | ||
MolProbity score | 1.19 | 1.44 |
Clashscore | 1.35 | 2.57 |
Poor rotamers (%) | 0.57 | 1.01 |
Ramachandran plot | ||
Favored (%) | 95.3 | 94.2 |
Allowed (%) | 3.7 | 5.3 |
Disallowed (%) | 1 | 0.5 |
