Table 1 Cryo-EM data collection, refinement and validation statistics
From: Molecular basis for selective uptake and elimination of organic anions in the kidney by OAT1
RnOat1 phosphate-bound state | RnOat1 α-KG-bound state | RnOat1 low-occupancy α-KG state | RnOat1 tenofovir-bound state | |
|---|---|---|---|---|
Data collection and processing | ||||
Magnification | ×105,000 | ×105,000 | ×105,000 | ×105,000 |
Voltage (kV) | 300 | 300 | 300 | 300 |
Electron exposure (e−/Å2) | 51 | 42 | 42 | 42 |
Defocus range (μm) | −1.0 to −2.0 | −0.8 to −2.0 | −0.8 to −2.0 | −0.8 to −2.0 |
Pixel size (Å) | 0.832 | 0.832 | 0.832 | 0.832 |
Symmetry imposed | C1 | C1 | C1 | C1 |
Initial particle images (no.) | 6,288,736 | 7,773,020 | 7,773,020 | 7,346,974 |
Final particle images (no.) | 458,380 | 240,196 | 202,820 | 210,734 |
Map resolution (Å) | 3.52 | 3.53 | 3.43 | 3.61 |
FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 |
Map resolution range (Å) | 3.0–33 | 3.0–21 | 2.9–32 | 3.1–10 |
Refinement | ||||
Initial model used | AlphaFold model (AF-O35956-F1) | |||
Model composition in the asymmetric unit | ||||
Nonhydrogen atoms | 4,806 | 4,748 | 4,737 | 4,799 |
Protein residues | 617 | 612 | 612 | 617 |
Ligandsa | 3 | 2 | 0 | 2 |
Average B factors (Å2) | ||||
Protein | 66.7 | 81.5 | 57.6 | 106.6 |
Ligand | 92.6 | 62.7 | 98.4 | |
r.m.s.d. | ||||
Bond lengths (Å) | 0.004 | 0.003 | 0.003 | 0.003 |
Bond angles (°) | 0.71 | 0.59 | 0.76 | 0.66 |
Validation | ||||
MolProbity score | 1.77 | 1.92 | 1.84 | |
Clashscore | 11.00 | 14.17 | 13.38 | |
Poor rotamers (%) | 0 | 0.98 | 0.78 | |
Ramachandran plot | ||||
Favored (%) | 95.40 | 96.69 | 96.19 | 96.72 |
Allowed (%) | 4.60 | 3.31 | 3.81 | 3.28 |
Outlier (%) | 0 | 0 | 0 | 0 |
