Table 1. Cryo-EM data collection, refinement, and validation statistics.
|
LicB:sybody C in nanodiscs
(PDB ID 7PAF, EMD-13268) |
|
| Data collection and processing | |
| Microscope | Glacios TEM |
| Camera | Gatan K3 GIF |
| Magnification | 46,000 |
| Voltage (kV) | 200 |
| Electron exposure (e−/Å2) | 50 |
| Defocus range (μm) | −0.5 to −3 |
| Pixel size (Å) | 0.878 |
| Symmetry imposed | C2 |
| Initial particle images (no.) | 3,113,507 |
| Final particle images (no.) | 78,649 |
| Map resolution (Å) | 3.75 |
| Fourier shell correlation (FSC) threshold |
0.143 |
| Map resolution range (Å) | 3.0–5.0 |
| 3D-FSC sphericity | 0.989 |
| Refinement | |
| Model resolution (Å) | 3.9 |
| FSC threshold | 0.5 |
| Map sharpening B-factor (Å2) | −75.8 |
| EMRinger score (LicB:sybody) | 2.59 |
| EMRinger score (LicB) | 3.25 |
| Model composition | |
| Nonhydrogen atoms | 6,009 |
| Protein residues | 780 |
| B-factors (Å2) | |
| Protein | 28.24 |
| POPG | 1.65 |
| RMSDs | |
| Bond lengths (Å) | 0.003 |
| Bond angles (°) | 0.631 |
| Validation | |
| MolProbity score | 1.91 |
| Clashscore | 13.19 |
| Poor rotamers (%) | 0.00 |
| Ramachandran plot | |
| Favored (%) | 95.92 |
| Allowed (%) | 3.82 |
| Disallowed (%) | 0.26 |
| CCmask | 0.73 |
| CCbox | 0.66 |
| CCvolume | 0.68 |
| CCpeaks | 0.55 |
| CCligands | 0.75 |