Table 1 Cryo-EM data collection, refinement and validation.
From: Structural ensemble of a glutamate transporter homologue in lipid nanodisc environment
Na+-only | Unsaturated 2in:1out | Unsaturated 2out:1in | Saturated | TBOA | |
|---|---|---|---|---|---|
Data collection and processing | |||||
Voltage (kV) | 200 | 200 | 200 | 200 | 200 |
Electron exposure (e−/Å2) | 53.3 | 53.3 | 53.3 | 53.3 | 53.3 |
Defocus range (μm) | −0.5 to −2.0 | −0.5 to −2.0 | −0.5 to −2.0 | −0.5 to −2.0 | −0.5 to −2.0 |
Pixel size (Å) | 1.012 | 1.012 | 1.012 | 1.012 | 1.012 |
Symmetry imposed | C1 | C1 | C1 | C3 | C1 |
Initial dataset (# of particles) | 1,193,046 | 348,173 | 348,173 | 444,955 | 578,728 |
Final dataset (# of particles) | 88,525 | 59,666 | 72,313 | 65,762 | 132,917 |
Map resolution (Å) FSC01.43 | 3.22 | 3.39 | 3.38 | 3.41 | 3.47 |
Refinement | |||||
Initial model used | PDB 5E9S | PDB 5E9S | PDB 5E9S | PDB 5E9S | PDB 5E9S |
Map-sharpening B factor (Å2) | 84.8 | 101.7 | 81.0 | 129.3 | 135.9 |
Model composition | |||||
Nonhydrogen atoms | 9564 | 9555 | 9552 | 9572 | 9547 |
Protein residues | 1278 | 1281 | 1280 | 1281 | 1276 |
Ligands | – | 1 | 2 | 3 | 2 |
Mean B factors (Å2) | |||||
Protein | 79.75 | 45.02 | 61.70 | 79.02 | 15.08 |
Ligand | – | 49.56 | 64.96 | 74.38 | 36.52 |
R.m.s. deviations | |||||
Bond lengths (Å) | 0.008 | 0.006 | 0.007 | 0.003 | 0.004 |
Bond angles (°) | 0.747 | 0.684 | 0.708 | 0.600 | 0.610 |
Validation | |||||
MolProbity score | 1.95 | 1.92 | 1.95 | 1.79 | 1.80 |
Clash score | 10.98 | 9.83 | 10.65 | 10.27 | 10.91 |
Poor rotamers (%) | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 |
Ramachandran plot (%) | |||||
Favored | 94.26 | 94.03 | 93.87 | 96.23 | 96.38 |
Allowed | 5.74 | 5.97 | 6.13 | 3.54 | 3.62 |
Outliers | 0.00 | 0.00 | 0.00 | 0.24 | 0.00 |
Model to map fit CC | 0.83 | 0.8 | 0.84 | 0.77 | 0.78 |
