Table 1. Cryo-EM data collection, refinement, and validation statistics.
|
5-HT–SERT
outward-NaCl (EMD-23365) (PDB 7LIA ) |
5-HT–SERT
occluded-NaCl (EMD-23830) (PDB 7MGW) |
5-HT–SERT
inward-KCl (EMD-23364) (PDB 7LI9) |
Apo SERT
occluded-NaCl (EMD-23362) (PDB 7LI7) |
Apo SERT
inward-NaCl (EMD-23363) (PDB 7LI8) |
Apo SERT
inward-KCl (EMD-23361) (PDB 7LI6) |
|
| Data collection and processing | ||||||
| Magnification | 77,160 | 62,383 | 77,160 | 75,642 | ||
| Voltage (kV) | 300 | 300 | 300 | 300 | ||
| Electron exposure (e−/Å2) |
55 | 57 | 50 | 52 | ||
| Defocus range (μm) | −0.8 to −2.5 | −0.9 to −2.7 | −1.0 to −2.5 | −1.0 to −2.5 | ||
| Pixel size (Å) | 0.648 | 0.802 | 0.648 | 0.661 | ||
| Symmetry imposed | C1 | C1 | C1 | C1 | C1 | C1 |
| Initial particle images (no.) |
2,861,741 | 5,624,930 | 5,568,431 | 5,865,511 | ||
| Final particle images (no.) |
774,907 | 114,222 | 299,808 | 636,335 | 343,085 | 707,210 |
| Map resolution (Å) | 3.1 | 3.5 | 3.7 | 3.9 | 3.9 | 3.5 |
| FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
| Map resolution range (Å) | 3.4–2.6 | 3.8–3.0 | 4.0–3.0 | 4.0–3.2 | 4.2–3.4 | 3.6–3.0 |
| Refinement | ||||||
| Initial model used (PDB code) |
6DZW | 6DZV | 6DZZ | 6DZV | 6DZZ | 6DZZ |
| Initial model CC | 0.59 | 0.78 | 0.83 | 0.56 | 0.74 | 0.64 |
| Model resolution (Å) | 3.5 | 4.0 | 3.9 | 4.1 | 4.2 | 3.8 |
| FSC threshold | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 |
| Map sharpening B factor (Å2) |
−178 | −157 | −161 | −214 | −195 | −185 |
| Model composition | ||||||
| Nonhydrogen atoms | 6,279 | 6,223 | 6,174 | 6,177 | 6,181 | 6,249 |
| Protein residues | 767 | 765 | 767 | 765 | 767 | 767 |
| Ligands (atoms) | 231 | 188 | 128 | 142 | 137 | 224 |
| B factors (Å2) | ||||||
| Protein | 28 | 192 | 29 | 98 | 99 | 73 |
| Ligand | 28 | 180 | 22 | 89 | 91 | 76 |
| Root mean square deviations | ||||||
| Bond lengths (Å) | 0.002 | 0.002 | 0.002 | 0.002 | 0.002 | 0.002 |
| Bond angles (°) | 0.422 | 0.470 | 0.444 | 0.470 | 0.461 | 0.444 |
| Validation | ||||||
| Refined model CC | 0.72 | 0.84 | 0.71 | 0.67 | 0.79 | 0.71 |
| MolProbity score | 1.71 | 1.75 | 1.70 | 1.81 | 1.74 | 1.81 |
| Clashscore | 7.98 | 8.97 | 6.00 | 10.00 | 6.76 | 5.29 |
| Poor rotamers (%) | 1.71 | 1.40 | 0.00 | 0.00 | 0.00 | 1.72 |
| Ramachandran plot | ||||||
| Favored (%) | 97.50 | 97.10 | 94.61 | 95.78 | 94.74 | 95.01 |
| Allowed (%) | 2.50 | 2.90 | 5.39 | 4.22 | 5.26 | 4.99 |
| Disallowed (%) | 0 | 0 | 0 | 0 | 0 | 0 |