Cryo-EM data collection, processing, and refinement statistics
| Data set . | Bent conformation . | Intermediate conformation . | Homodimer conformation . |
|---|---|---|---|
| Data collection and processing | |||
| Magnification | 81 000 | ||
| Voltage (kV) | 300 | ||
| Electron microscope | Krios-GIF-K3 | ||
| Defocus range | −0.8 to 1.5 | ||
| Total exposure time (s) | 4 | ||
| Pixel size (Å) | 1.07 | ||
| Total dose (e−/A2) | 37.3 | ||
| No. of frames | 40 | ||
| Dose rate (e−/phys. pixel/s) | 11.71 | ||
| No. of initial micrographs | 13 807 | ||
| No. of initial particles | 17 985 649 | ||
| No. of final particles | 120 965 | 518 071 | 274 866 |
| Symmetry | C1 | C1 | C1 |
| GS-FSC resolution (Å) | 2.75 | 2.67 | 2.85 |
| FSC threshold | 0.143 | ||
| Refinement | |||
| Initial model | AlphaFold | ||
| Model resolution cutoff (Å) | 0.1 | 0.1 | 0.1 |
| No. of protein residues | 1602 | 1106 | 2196 |
| No. of ligands | Ca = 7 | Ca = 6 | Ca = 12 |
| Mg = 1 | Mg = 1 | Mg = 2 | |
| NAG = 18 | NAG =, 10 | NAG = 18 | |
| BMA = 4 | BMA = 3 | BMA = 3 | |
| RMSD | |||
| Bond lengths (Å) | 0.005 | 0.007 | 0.004 |
| Bond angles (°) | 0.704 | 0.861 | 0.650 |
| Validation | |||
| MolProbity score | 2.56 | 2.13 | 2.66 |
| Clash score | 25.16 | 10.81 | 15.26 |
| Rotamer outliers (%) | 2.49 | 1.73 | 4.59 |
| Ramachandran plot (%) | |||
| Favored (%) | 94.59 | 94.19 | 92.49 |
| Allowed (%) | 5.22 | 5.63 | 7.19 |
| Disallowed (%) | 0.19 | 0.18 | 0.32 |
| Data set . | Bent conformation . | Intermediate conformation . | Homodimer conformation . |
|---|---|---|---|
| Data collection and processing | |||
| Magnification | 81 000 | ||
| Voltage (kV) | 300 | ||
| Electron microscope | Krios-GIF-K3 | ||
| Defocus range | −0.8 to 1.5 | ||
| Total exposure time (s) | 4 | ||
| Pixel size (Å) | 1.07 | ||
| Total dose (e−/A2) | 37.3 | ||
| No. of frames | 40 | ||
| Dose rate (e−/phys. pixel/s) | 11.71 | ||
| No. of initial micrographs | 13 807 | ||
| No. of initial particles | 17 985 649 | ||
| No. of final particles | 120 965 | 518 071 | 274 866 |
| Symmetry | C1 | C1 | C1 |
| GS-FSC resolution (Å) | 2.75 | 2.67 | 2.85 |
| FSC threshold | 0.143 | ||
| Refinement | |||
| Initial model | AlphaFold | ||
| Model resolution cutoff (Å) | 0.1 | 0.1 | 0.1 |
| No. of protein residues | 1602 | 1106 | 2196 |
| No. of ligands | Ca = 7 | Ca = 6 | Ca = 12 |
| Mg = 1 | Mg = 1 | Mg = 2 | |
| NAG = 18 | NAG =, 10 | NAG = 18 | |
| BMA = 4 | BMA = 3 | BMA = 3 | |
| RMSD | |||
| Bond lengths (Å) | 0.005 | 0.007 | 0.004 |
| Bond angles (°) | 0.704 | 0.861 | 0.650 |
| Validation | |||
| MolProbity score | 2.56 | 2.13 | 2.66 |
| Clash score | 25.16 | 10.81 | 15.26 |
| Rotamer outliers (%) | 2.49 | 1.73 | 4.59 |
| Ramachandran plot (%) | |||
| Favored (%) | 94.59 | 94.19 | 92.49 |
| Allowed (%) | 5.22 | 5.63 | 7.19 |
| Disallowed (%) | 0.19 | 0.18 | 0.32 |
BMA, beta-D-mannose; Ca, calcium; Mg, magnesium; NAG, N-acetylglucosamine.