Table 1 Cryo-EM data collection, refinement and validation statistics
From: Cryo-EM reveals how Hsp90 and FKBP immunophilins co-regulate the glucocorticoid receptor
Data collection and processing | Dataset I | Dataset II | Dataset III | Dataset IV |
Magnification | 105,000 | 105,000 | 105,000 | 105,000 |
Voltage (kV) | 300 | 300 | 300 | 300 |
Electron exposure (e– Å−2) | 69 | 69 | 69 | 45.8 |
Defocus range (μm) | 0.8–2.0 | 0.8–2.0 | 0.8–2.0 | 0.8–2.0 |
Pixel size (Å) | 0.835 | 0.835 | 0.835 | 0.835 |
Symmetry imposed | C1 | C1 | C1 | C1 |
Initial particle images (no.) | 4,736387 | 2,783,284 | 3,788,005 | 6,268,573 |
Consensus map resolution (Å) | 3.01 | 3.23 | ||
FSC threshold | 0.143 | 0.143 | ||
Map resolution range (Å) | 2.44–7.73 | 2.66–9.62 | ||
Final particle images (no.) | 307,109 | 171,778 | ||
Hsp90 focused map resolution (Å) | 2.96 | 3.19 | ||
FSC threshold | 0.143 | 0.143 | ||
Final particle images (no.) | 307,109 | 171,778 | ||
GR:FKBP focused map resolution (Å) | 3.76 | 4.14 | ||
FSC threshold | 0.143 | 0.143 | ||
Final particle images (no.) | 106,318 | 109,900 | ||
Refinement | ||||
Initial model (PDB/AlphaFold code) | 7KRJ, AF-Q02790, 5NJX | 7KRJ, 7L7I, 5NJX | ||
Model resolution (Å) | 3.13 | 3.61 | ||
FSC threshold | 0.5 | 0.5 | ||
Map sharpening B factor (Å2) | −30 | −30 | ||
Model composition | ||||
Non-hydrogen atoms | 15,829 | 15,756 | ||
Protein residue atoms | 15,737 | 15,664 | ||
Ligand atoms | 92 | 92 | ||
Mean B factors [min–max] (Å2) | ||||
Protein | 209.15 [0.03–600.0] | 244.41 [60.07–600.0] | ||
Ligand | 140.07 [15.18–409.30] | 222.63 [75.96–528.72] | ||
Root mean square deviations | ||||
Bond lengths (Å) | 0.023 | 0.024 | ||
Bond angles (°) | 1.837 | 1.936 | ||
Validation | ||||
MolProbity score | 0.81 | 0.84 | ||
Clashscore | 1.07 | 1.24 | ||
Poor rotamers (%) | 0.00 | 0.00 | ||
Ramachandran plot | ||||
Favored (%) | 98.70 | 98.55 | ||
Allowed (%) | 1.19 | 1.40 | ||
Disallowed (%) | 0.10 | 0.05 | ||
