Table 1 Cryo-EM data collection, refinement and validation statistics of the ETB receptor-Gi complexes
From: Structure of endothelin ETB receptor–Gi complex in a conformation stabilized by unique NPxxL motif
ET-1 bound ETBR-DNGi-scFv16 (EMDB-38740, PDB-8XWP) | ET-1 bound ETBR-DNGi-scFv16 (focused ETBR) (EMDB-60404, PDB-8ZRT) | ET-1 bound ETBR-wild type Gi-scFv16 (EMDB-38741, PDB-8XWQ) | ||
|---|---|---|---|---|
Data collection and processing | ||||
Microscope | JEOL CRYO-ARM300 | TF Talos Arctica | ||
Camera | K3 | Falcon III | ||
Magnification | 60,000 | 100,000 | 92,000 | |
Voltage (kV) | 300 | 300 | 200 | |
Electron exposure (e–/Å2) | 53.3 | 49.2 | 40 | |
Defocus range (μm) | –0.5 to –2.7 | –0.6 to –3.5 | –0.7 to –2.9 | |
Calibrated pixel size (Å) | 0.816 | 0.507 | 1.094 | |
Detector physical pixel size (μm) | 5 | 14 | ||
Symmetry imposed | C1 | C1 | ||
Initial particle images (no.) | 1,193,302 | 1,757,339 | 1,038,215 | 954,972 |
Final particle images (no.) | 556,576 | 481,639 | 401,671 | 278,209 |
Map resolution (Å) | 3.2 | 3.6 | 4.6 | |
FSC threshold | 0.143 | 0.143 | 0.143 | |
Map resolution range (Å) | 5.4–3.1 | 8.7–3.6 | 6.9–4.4 | |
Refinement | ||||
Initial model used (PDB code) | 5GLH, 6OS9 | 8XWP | 5GLH, 6OS9 | |
Model resolution (Å) | 3.2 | 4.1 | 4.6 | |
FSC threshold | 0.5 | 0.5 | 0.5 | |
Model resolution range (Å) | 120–3.2 | 120–3.6 | 126–4.6 | |
Map sharpening B factor (Å2) | –100 | -100 | –263 | |
Model composition | ||||
Non-hydrogen atoms | 9076 | 2322 | 9076 | |
Protein residues | 1163 | 303 | 1163 | |
B factors (Å2) | ||||
Protein | 80.7 | 48.9 | 191.8 | |
R.m.s. deviations | ||||
Bond lengths (Å) | 0.002 | 0.003 | 0.003 | |
Bond angles (°) | 0.473 | 0.693 | 0.546 | |
Validation | ||||
MolProbity score | 2.31 | 1.82 | 2.59 | |
Clashscore | 8.97 | 13.56 | 14.24 | |
Poor rotamers (%) | 5.56 | 0.81 | 7.98 | |
Ramachandran plot | ||||
Favored (%) | 96.06 | 96.93 | 96.33 | |
Allowed (%) | 3.94 | 3.07 | 3.67 | |
Disallowed (%) | 0.00 | 0.00 | 0.00 | |
