Table 1 Cryo-EM data collection, refinement and validation statistics
From: Molecular basis of plastoquinone reduction in plant cytochrome b6f
Cytb6f + DPQ | Cytb6f + DPQ + DPQH2 + PC | Cytb6f + DBMIB | |
|---|---|---|---|
PDB ID 9ES7 | PDB ID 9ES8 | PDB ID 9ES9 | |
EMD 19938 | EMD 19939 | EMD 19940 | |
Data collection and processing | |||
Magnification of exposure image | ×105,000 | ×105,000 | ×105,000 |
Operating voltage (kV) | 300 | 300 | 300 |
Electron exposure (e− Å−2) | 40.70 | 40.70 | 41.34 |
Defocus range (µm) | −2.1 to −0.9 | −2.1 to −0.9 | −2.1 to −0.9 |
Pixel size (Å) | 0.86 | 0.86 | 0.86 |
Symmetry imposed | C2 | C2 | C2 |
Final particle images | 1,320,078 | 482,950 | 389,849 |
Map resolution (Å) | 1.94 | 2.24 | 2.33 |
FSC threshold | 0.143 | 0.143 | 0.143 |
Map resolution range (Å) | 1.9 to >10 | 1.9 to >10 | 1.9 to >10 |
Refinement | |||
Initial model used (PDB ID) | |||
Model resolution (Å) | 2.1 | 2.1 | 2.1 |
FSC threshold | 0.143 | 0.143 | 0.143 |
Model resolution range (Å) | NA | NA | NA |
Map sharpening B factor (Å2) | 58.3 | 71.3 | 72.5 |
Model composition | |||
Non-hydrogen atoms | 16,413 | 16,326 | 16,450 |
Protein residues | 1,950 | 1,948 | 1,974 |
Ligands | 22 | 24 | 24 |
Water molecules | 329 | 214 | 206 |
B factors (Å2) | |||
Protein | 56.97 | 76.03 | 80.93 |
Ligands | 55.97 | 80.25 | 85.03 |
Water molecules | 57.21 | 71.37 | 78.49 |
RMS deviations | |||
Bond lengths (Å) | 0.003 | 0.003 | 0.004 |
Bond angles (°) | 0.514 | 0.482 | 0.983 |
Validation | |||
MolProbity score | 0.94 | 0.99 | 1.31 |
Clashscore | 1.81 | 1.72 | 3.25 |
Poor rotamers (%) | 0.37 | 0.37 | 0.61 |
Ramachandran | |||
Favoured (%) | 98.43 | 97.69 | 96.79 |
Allowed (%) | 1.57 | 2.31 | 3.21 |
Disallowed (%) | 0 | 0 | 0 |
CC volume | 0.90 | 0.88 | 0.87 |
