Table 2.
Cryo-EM data collection, refinement and validation statistics
| GluA2–γ5–CNIH2ZK-PMP-SPD LBD–TMD (EMDB-40746) (PDB 8SS7) |
GluA2–γ5ZK-PMP FL (EMDB-40747) (PDB 8SS8) |
GluA2–γ5ZK-PMP LBD–TMD (EMDB-40748) (PDB 8SS9) |
GluA2–γ5–CNIH2Glu-SPD FL (EMDB-40749) (PDB 8SSA) |
GluA2–γ5–CNIH2Glu-SPD LBD–TMD (EMDB-40750) (PDB 8SSB) |
|
|---|---|---|---|---|---|
| Data collection and processing | |||||
| Magnification | ×75,000 | ×75,000 | ×75,000 | ×105,000 | ×105,000 |
| Voltage (kV) | 300 | 300 | 300 | 300 | 300 |
| Electron exposure (e−/Å2) | 50 | 50 | 50 | 58 | 58 |
| Defocus range (μm) | −1 to −2 | −1 to −2 | −1 to −2 | −1 to −2 | −1 to −2 |
| Pixel size (Å) | 0.925 | 0.925 | 0.925 | 0.83 | 0.83 |
| Symmetry imposed | C2 | C2 | C2 | C2 | C2 |
| Initial particle images (no.) | 2,360,956 | 2,360,956 | 2,360,956 | 2,282,408 | 2,282,408 |
| Final particle images (no.) | 126,263 | 126,964 | 117,939 | 58,186 | 48,434 |
| Map resolution (Å) | 2.76 | 2.81 | 2.72 | 3.88 | 3.66 |
| FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
| Map resolution range (Å) | 2.6/3.3/34.4 | 2.0/3.3/36.3 | 2.0/3.3/36.0 | 2.1/5.8/42.5 | 2.1/4.8/36.5 |
| Refinement | |||||
| Initial model used (PDB code) | 7RZ5, 7OCE | 7RZ5, 7OCE | 7RZ5, 7OCE | 7RZ5, 7OCE | 7RZ5, 7OCE |
| Model resolution (Å) | 2.76 | 2.81 | 2.72 | 3.88 | 3.66 |
| FSC threshold | |||||
| Map sharpening B factor (Å2) | −132.7 | −135.5 | −131.4 | −101.4 | −97.2 |
| Model composition | |||||
| Nonhydrogen atoms | 19,436 | 28,487 | 16,319 | 30,888 | 19,048 |
| Protein residues | 2,266 | 3,514 | 1,986 | 3,840 | 2,304 |
| Ligands | |||||
| PMP | 4 | 4 | 4 | – | – |
| SPD | 1 | – | – | 1 | 1 |
| ZK | 4 | 4 | 4 | – | – |
| Glutamate (Glu) | – | – | – | 4 | 4 |
| B factors (Å2) | |||||
| Protein | 63.09 | 68.50 | 65.55 | 128.43 | 68.50 |
| Ligand | 41.07 | 98.06 | 65.93 | 66.30 | 98.06 |
| R.m.s. deviations | |||||
| Bond lengths (Å) | 0.010 | 0.014 | 0.008 | 0.010 | 0.007 |
| Bond angles (°) | 1.657 | 1.585 | 1.541 | 1.431 | 1.376 |
| Validation | |||||
| MolProbity score | 1.92 | 1.75 | 1.51 | 1.96 | 2.01 |
| Clashscore | 6.95 | 3.86 | 4.43 | 6.33 | 7.27 |
| Poor rotamers (%) | 1.45 | 1.33 | 0.36 | 1.00 | 0.72 |
| Ramachandran plot | |||||
| Favored (%) | 93.80 | 92.19 | 95.80 | 87.63 | 87.37 |
| Allowed (%) | 5.66 | 7.12 | 3.89 | 11.37 | 11.40 |
| Disallowed (%) | 0.54 | 0.69 | 0.31 | 1.00 | 1.24 |