Table 1 Cryo-EM data collection, refinement and validation statistics for the MpPSI-LHCI supercomplexes
From: Structural study of monomeric and dimeric photosystem I-LHCI supercomplexes from a bryophyte
Data collection and processing | PSI-LHCI monomer (EMDB-63404) (PDB 9LUT) | PSI-LHCI dimer (EMDB-63405) (PDB 9LUU) |
|---|---|---|
Magnification | 165,000 | 165,000 |
Voltage (kV) | 300 | 300 |
Electron exposure (e− Å−2) | 50 | 50 |
Defocus range (µm) | −0.8 to −2.0 | −0.6 to −1.8 |
Pixel size (Å) | 0.727 | 0.727 |
Symmetry imposed | C1 | C2 |
Initial particle images (no.) | 1,078,038 | 2,140,369 |
Final particle images (no.) | 157,648 | 25,750 |
Map resolution (Å) | 1.94 | 2.52 |
FSC threshold | 0.143 | 0.143 |
Map resolution range (Å) | 1.94–2.8 | 2.52–3.9 |
Refinement | ||
Initial model used (PDB code) | 6L35 | This study |
Model resolution (Å) | 2.13 | 2.94 |
FSC threshold | 0.5 | 0.5 |
Model resolution range (Å) | 2.13–2.26 | 3.04–3.20 |
Model-sharpening B factor (Å2) | −26.9 | −30.7 |
Model composition | ||
Non-hydrogen atoms | 36,238 | 69,774 |
Protein residues | 3,217 | 6,430 |
Ligands | 207 | 400 |
Unknown Ligand | 0 | 4 |
Water | 606 | 0 |
B factors (Å2) | ||
Protein | 61.60 | 96.03 |
Ligand | 59.05 | 90.74 |
Water | 57.07 | - |
R.m.s. deviations | ||
Bond lengths (Å) | 0.007 | 0.008 |
Bond angle (˚) | 1.471 | 1.637 |
Validation | ||
MolProblity | 1.54 | 1.77 |
Clash score | 5.98 | 7.70 |
Rotamer outliers (%) | 1.35 | 1.50 |
Ramachandran plot | ||
Favored (%) | 97.42 | 96.66 |
Allowed (%) | 2.49 | 3.34 |
Disallowed (%) | 0.09 | 0.00 |
