Table 1 Cryo-EM data collection, refinement and validation statistics
From: Cryo-EM structures of ρ1 GABAA receptors with antagonist and agonist drugs
PDB ID | 9FRE | 9FRB | 9FRF | 9FRI | 9FRF | 9FRG |
|---|---|---|---|---|---|---|
Ligand | THIP | CGP | (R)-GABOB | (S)-GABOB | (R)-GABOB | (S)-GABOB |
Apparent state | Resting-like | Resting-like | Partially locked | Partially locked | De-sensitized | De-sensitized |
Data collection and processing | ||||||
Magnification | 130,000 | 130,000 | 130,000 | |||
Voltage (kV) | 300 | 300 | 300 | |||
Electron exposure (e–/Å2) | 48.3 | 44.0 | 47.0 | |||
Defocus range (μm) | −0.8 to −1.8 | −0.8 to −1.8 | −0.8 to −1.8 | |||
Pixel size (Å) | 0.6725 | 0.6725 | 0.67 | |||
Symmetry imposed | C5 | C5 | C5 | C5 | ||
Final particles | 135,764 | 398,556 | 191,614 | 57,366 | ||
Map resolution (Å) | 2.19 | 2.05 | 2.14 | 2.41 | ||
FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | ||
Refinement | ||||||
Map sharpening B factor (Å2) | −66.2 | −63.6 | −66 | −70.8 | ||
Non-hydrogen atoms | 14,491 | 14,402 | 13,756 | 13,756 | 13,882 | 13,882 |
Protein residues | 1670 | 1665 | 1660 | 1660 | 1645 | 1645 |
Ligands | 56 | 57 | 56 | 56 | 42 | 42 |
B factors (Å2) | ||||||
Protein | 31.59 | 10.02 | 14.49 | 11.03 | 41.01 | 41.01 |
Ligand | 57.41 | 24.84 | 32.35 | 24.08 | 71.63 | 70.76 |
R.m.s. deviations | ||||||
Bond lengths (Å) | 0.004 | 0.007 | 0.006 | 0.006 | 0.007 | 0.007 |
Bond angles (°) | 0.879 | 0.828 | 1.211 | 1.219 | 1.168 | 1.171 |
Validation | ||||||
MolProbity score | 1.32 | 0.99 | 1.68 | 1.68 | 0.88 | 0.88 |
Clashscore | 4.51 | 2.14 | 5.41 | 5.41 | 0.58 | 0.58 |
Poor rotamers (%) | 0.00 | 0.00 | 0.63 | 0.7 | 0.00 | 0.00 |
Ramachandran plot | ||||||
Favored (%) | 97.58 | 98.48 | 94.21 | 94.21 | 96.92 | 96.92 |
Allowed (%) | 2.42 | 1.52 | 5.49 | 5.49 | 3.08 | 3.08 |
Disallowed (%) | 0.00 | 0.00 | 0.30 | 0.30 | 0.00 | 0.00 |
