Table 1.
Cryo-EM data collection, refinement and validation statistics.
| System xc− (EMD-13267) (PDB 7P9V) | System xc− + glutamate (EMD-13266) (PDB 7P9U) | |
|---|---|---|
| Data collection and processing | ||
| Magnification | 105,000 | 105,000 |
| Voltage (kV) | 300 | 300 |
| Electron exposure (e–/Å2) | 59.1 | 59.1 |
| Defocus range (μm) | 0.8–2.5 | 0.8–2.5 |
| Pixel size (Å) | 0.832 | 0.832 |
| Symmetry imposed | C1 | C1 |
| Initial particle images (no.) | 8,763,822 | 8,820,414 |
| Final particle images (no.) | 300,221 | 79,698 |
| Map resolution (Å) | 3.4 | 3.7 |
| FSC threshold | 0.143 | 0.143 |
| Map resolution range (Å) | 3.3–4.1 | 3.6–4.7 |
| Refinement | ||
| Initial model used (PDB code) | None | None |
| Model resolution (Å) | 3.4 | 3.7 |
| FSC threshold | 0.143 | 0.143 |
| Model resolution range (Å) | 3.3–4.1 | 3.6–4.7 |
| Map sharpening B factor (Å2) | −81.5 | −74.4 |
| Model composition | ||
| Non-hydrogen atoms | 7286 | 3933 |
| Protein residues | 919 | 502 |
| Ligands | NAG: 8 | GLU: 1 |
| B factors (Å2) | ||
| Protein | 67.17 | 90.04 |
| Ligand | 99.12 | 75.62 |
| R.m.s. deviations | ||
| Bond lengths (Å) | 0.005 | 0.003 |
| Bond angles (°) | 0.803 | 0.678 |
| Validation | ||
| MolProbity score | 2.28 | 2.02 |
| Clashscore | 15.39 | 11.18 |
| Poor rotamers (%) | 0.00 | 0.00 |
| Ramachandran plot | ||
| Favoured (%) | 88.52 | 92.77 |
| Allowed (%) | 11.48 | 6.83 |
| Disallowed (%) | 0.00 | 0.40 |