Table 2. Cryo-electron microscopy (cryo-EM) data collection, refinement, and validation statistics.
| Native RC-LH at 180 μmol m–2 s–1(nRC-LH)(EMD-34838)(PDB 8HJU) | Carotenoid-depleted RC-LH at 180 μmol m–2 s–1(dRC-LH)(EMD-34839)(PDB 8HJV) | |
|---|---|---|
| Data collection and processing | ||
| Magnification | 64,000 | 81,000 |
| Voltage (kV) | 300 | 300 |
| Electron exposure (e–/Å2) | 50 | 49.65 |
| Defocus range (μm) | –1.0 to –2.3 | –1.1 to –1.7 |
| Pixel size (Å) | 1.08 | 0.893 |
| Symmetry imposed | C1 | C1 |
| Initial particle images (no.) | 1,625,156 | 1,081,719 |
| Final particle images (no.) | 372,029 | 84,352 |
| Map resolution (Å) FSC threshold |
2.8 0.143 |
3.1 0.143 |
| Refinement | ||
| Initial model used (PDB code) | 5YQ7 | Native RC-LH |
| Model resolution (Å) FSC threshold |
2.8 0.5 |
3.1 0.5 |
| Map sharpening B factor (Å2) | 98 | 120 |
| Model composition Non-hydrogen atoms Protein residues Ligands |
23,917 2330 97 |
22,193 2265 67 |
|
B factors (Å2) Protein Ligand |
35.81 32.21 |
52.46 55.37 |
| R.m.s. deviations Bond lengths (Å) Bond angles (°) |
0.011 1.509 |
0.010 1.205 |
| Validation MolProbity score Clashscore Poor rotamers (%) |
2.00 16.11 0.71 |
2.17 18.87 0.84 |
| Ramachandran plot Favored (%) Allowed (%) Disallowed (%) |
95.83 4.17 0.00 |
94.16 5.75 0.09 |
| Native RC-LH at 2 μmol m–2 s–1(EMD-35988)(PDB 8J5O) | Native RC-LH at 32 μmol m–2 s–1(EMD-35989)(PDB 8J5P) | |
| Data collection and processing | ||
| Magnification | 81,000 | 81,000 |
| Voltage (kV) | 300 | 300 |
| Electron exposure (e–/Å2) | 50 | 50 |
| Defocus range (μm) | –1.2 to –2.0 | –1.2 to –2.0 |
| Pixel size (Å) | 0.893 | 0.893 |
| Symmetry imposed | C1 | C1 |
| Initial particle images (no.) | 779,594 | 686,082 |
| Final particle images (no.) | 322,595 | 272,617 |
| Map resolution (Å) FSC threshold |
2.9 0.143 |
3.1 0.143 |
| Refinement | ||
| Initial model used (PDB code) | 8HJU | 8HJU |
| Model resolution (Å) FSC threshold |
2.8 0.5 |
3.1 0.5 |
| Map sharpening B factor (Å2) | 98 | 120 |
| Model composition Non-hydrogen atoms Protein residues Ligands |
23,691 2318 93 |
23,737 2331 92 |
|
B factors (Å2) Protein Ligand |
27.54 24.73 |
39.01 37.37 |
| R.m.s. deviations Bond lengths (Å) Bond angles (°) |
0.018 1.915 |
0.017 1.850 |
| Validation MolProbity score Clashscore Poor rotamers (%) |
1.97 18.79 0.00 |
1.98 17.69 0.30 |
| Ramachandran plot Favored (%) Allowed (%) Disallowed (%) |
96.79 3.21 0.00 |
96.50 3.46 0.04 |