Table 1.
Cryo-EM data collection, refinement and validation statistics of the Alc. vinosum LH1–RC complexes.
| Sucrose-density purified LH1–RC complex (EMDB-37465, PDB-8WDU) | Ca2+-DEAE purified LH1–RC complex (EMDB-37466, PDB-8WDV) | |
|---|---|---|
| Data collection and processing | ||
| Microscope | JEOL CRYO-ARM300II | TF Titan Krios |
| Camera | K3 | Falcon III |
| Magnification | 80,000 | 96,000 |
| Voltage (kV) | 300 | 300 |
| Electron exposure (e–/Å2) | 50 | 40 |
| Defocus range (μm) | −0.7 to −3.2 | −0.5 to −2.6 |
| Calibrated pixel size (Å) | 0.606 | 0.82 |
| Detector physical pixel size (μm) | 5 | 14 |
| Symmetry imposed | C1 | C1 |
| Initial particle images (no.) | 361,654 | 833,998 |
| Final particle images (no.) | 252,230 | 219,233 |
| Map resolution (Å) | 2.2 | 2.2 |
| FSC threshold | 0.143 | 0.143 |
| Map resolution range (Å) | 3.2–2.2 | 4.3–2.1 |
| Refinement | ||
| Initial model used (PDB code) | 7VRJ | 7VRJ |
| Model resolution (Å) | 2.3 | 2.3 |
| FSC threshold | 0.5 | 0.5 |
| Model resolution range (Å) | 135–2.2 | 135–2.2 |
| Map sharpening B factor (Å2) | –44 | –63 |
| Model composition | ||
| Non-hydrogen atoms | 26,274 | 26,261 |
| Protein residues | 2575 | 2585 |
| Ligands | 113 | 111 |
| Waters | 334 | 354 |
| B factors (Å2) | ||
| Protein | 27.4 | 45.9 |
| Ligand | 30.3 | 51.2 |
| Water | 23.6 | 47.8 |
| R.m.s. deviations | ||
| Bond lengths (Å) | 0.006 | 0.006 |
| Bond angles (°) | 2.821 | 2.796 |
| Validation | ||
| MolProbity score | 1.77 | 1.61 |
| Clashscore | 12.15 | 12.55 |
| Poor rotamers (%) | 1.63 | 0.98 |
| Ramachandran plot | ||
| Favored (%) | 97.95 | 98.2 |
| Allowed (%) | 2.05 | 1.8 |
| Disallowed (%) | 0 | 0 |