Table 1 Cryo-EM data collection, refinement, and validation statistics
From: Cryo-EM structures of the channelrhodopsin ChRmine in lipid nanodiscs
| Â | ChRmine small nanodisc (PDB 7SFK) (EMDB 25091) | ChRmine large nanodisc (PDB 7SFJ) (EMDB 25079) | apo-ChRmine nanodisc (PDB 7SHS) (EMDB 25135) |
|---|---|---|---|
Data collection and processing | |||
Magnification | ×36,000 | ×36,000 | ×36,000 |
Voltage (kV) | 200 | 200 | 200 |
Electron exposure (e–/Å2) | 50 | 50 | 50 |
Defocus range (μm) | −0.6 to −2.0 | −0.6 to −2.0 | −0.6 to −2.0 |
Super resolution pixel size (Ã…) | 0.5685 | 0.5685 | 0.5685 |
Binned pixel size (Ã…) | 1.137 | 1.137 | 1.137 |
Symmetry imposed | C3 | C3 | C1 |
Initial particle images (no.) | 8,444,523 | 8,444,523 | 7,054,805 |
Final particle images (no.) | 81,839 | 100,946 | 41,053 |
Map resolution (Ã…) | 2.7 | 3.1 | 4.1 |
 FSC threshold | 0.143 | 0.143 | 0.143 |
Refinement | |||
Initial model used (PDB code) | de novo | de novo | 7SFK |
Model resolution (Ã…) | 2.7 | 3.0 | 4.1 |
 FSC threshold | 0.143 | 0.143 | 0.143 |
Model composition | |||
 Nonhydrogen atoms | 7419 | 7377 | 6873 |
 Protein residues | 852 | 852 | 849 |
 Ligands | 24 | 24 | 0 |
 Waters | 57 | 3 | 0 |
Mean B factors (Ã…2) | |||
 Protein | 14.21 | 59.86 | 149.44 |
 Ligand | 20.21 | 58.10 | – |
 Water | 16.05 | 51.81 | – |
R.m.s. deviations | |||
 Bond lengths (Å) | 0.003 | 0.003 | 0.003 |
 Bond angles (°) | 0.536 | 0.537 | 0.740 |
CC mask | 0.85 | 0.79 | 0.70 |
Validation | |||
MolProbity score | 1.15 | 1.27 | 1.33 |
Clashscore | 3.61 | 3.87 | 5.95 |
Poor rotamers (%) | 0.43 | 0.85 | 0 |
Ramachandran plot | |||
 Favored (%) | 98.22 | 97.51 | 98.22 |
 Allowed (%) | 1.78 | 2.49 | 1.78 |
 Disallowed (%) | 0 | 0 | 0 |
