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 |
