Table 1 Cryo-EM data collection and refinement statistics
From: Structural basis of ligand recognition and design of antihistamines targeting histamine H4 receptor
H4R/Histamine/Gi | H4R/Clobenpropit/Gi | H4R/VUF6884/Gi | H4R/Clozapine/Gi | |
|---|---|---|---|---|
EMD-36712 | EMD-36716 | EMD-36715 | EMD-36714 | |
8JXT | 8JXX | 8JXW | 8JXV | |
Data collection and processing | ||||
Magnification | 130,000 | 130,000 | 130,000 | 64,000 |
Voltage (kV) | 300 | 300 | 300 | 300 |
Electron exposure (e-/Å2) | 60 | 60 | 60 | 50 |
Defocus range (µm) | 1.2–2.2 | 1.2–2.2 | 1.2–2.2 | 1.8 |
Pixel size (Å) | 1.1 | 1.1 | 1.1 | 1.08 |
Symmetry imposed | C1 | C1 | C1 | C1 |
Initial particle image (no.) | 1.9 M | 1.0 M | 1.7 M | 1.5 M |
Final particle image (no.) | 340k | 86k | 334k | 106k |
Map resolution (Å) | 3.07 | 3.06 | 3.01 | 3.21 |
FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 |
Refinement | ||||
Initial model used (PDB code) | AlphaFold-Q9H3N8-v1 | AlphaFold-Q9H3N8-v1 | AlphaFold-Q9H3N8-v1 | AlphaFold-Q9H3N8-v1 |
Model Resolution (Å) | NA | NA | NA | NA |
Map sharpening B factor (Å2) | –129.4 | –91.6 | –107.4 | –116.7 |
Model composition | ||||
Non-hydrogen atoms | 8294 | 8385 | 8389 | 7935 |
Protein residues | 1107 | 1108 | 1109 | 1040 |
Ligands | 1 | 1 | 1 | 1 |
B factor (Å2) | ||||
Protein | 68.27 | 80.03 | 76.63 | 56.73 |
Ligand | 0 | 86.36 | 78.07 | 30.06 |
R.m.s. deviations | ||||
Bond length (Å) | 0.005 | 0.006 | 0.006 | 0.006 |
Bond angles (°) | 1.044 | 0.746 | 0.795 | 0.78 |
Validation | ||||
MolProbity score | 1.86 | 1.61 | 1.64 | 2 |
Clashscore | 7.01 | 5.09 | 6.24 | 12.39 |
Poor rotamers (%) | 0 | 0 | 0 | 0 |
Ramachandran plot | ||||
Favored (%) | 94.58 | 95.13 | 95.77 | 94.19 |
Allowed (%) | 5.42 | 4.87 | 4.23 | 5.81 |
Disallowed | 0 | 0 | 0 | 0 |
