Table 1.
Cryo-EM data collection, refinement and validation statistics
| Composite map of isolated RS1 (EMD-22475, PDB 7JTK) | Composite map of RS2 stalk–IDAc–N-DRC/DMT (EMD-22481, PDB 7JU4) | On-doublet RS1 stalk (EMD-22480, PDB 7JTS) | On-doublet RS1 spokehead (EMD-22482) | On-doublet RS2 spokehead (EMD-22483) | On-doublet RSP1 dimer (EMD-22486) | |
|---|---|---|---|---|---|---|
| Data collection and processing | ||||||
| Magnification | 81,000 | 81,000 | 81,000 | 81,000 | 81,000 | 81,000 |
| Voltage (kV) | 300 | 300 | 300 | 300 | 300 | 300 |
| Electron exposure (e−/Å2) | 60.0 | 38.9 | 38.9 | 38.9 | 38.9 | 38.9 |
| Defocus range (μm) | −1.1 to −2.4 | −1.0 to −3.5 | −1.0 to −3.5 | −1.0 to −3.5 | −1.0 to −3.5 | −1.0 to −3.5 |
| Pixel size (Å) | 1.09 | 1.403 | 1.403 | 1.403 | 1.403 | 1.403 |
| Symmetry imposed | C1 | C1 | C1 | C1 | C1 | C1 |
| Initial particle images (no.) | 2,320,543 | 202,168* | 202,168 | 202,168 | 202,168 | 202,168 |
| Final particle images (no.) | 221,836 | 202,168 | 143,514 | 95,932 | 121,492 | 49,714 |
| Map resolution (Å) | 3.2 - 3.7† | 3.4 - 4.1 | 6.1 | 5.3 | 4.6 | 6.3 |
| FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
| Refinement | ||||||
| Map sharpening B factor (Å2) | −74 to −32† | −139 to −50 | −100 | −127 | −160 | −300 |
| Model composition | ||||||
| Non-hydrogen atoms | 72,807 | 133,504 | 6,801 | - | - | - |
| Protein residues | 9,516 | 17,032 | 1,377 | - | - | - |
| Ligands | 4 PO4 | 14 GDP / 14 GTP / 14 Mg / 1 ATP | - | - | - | - |
| B factors (Å2) | ||||||
| Protein | 30.8 | 61.56 | 17.62 | - | - | - |
| Ligand | 50 | 51.4 | - | - | - | - |
| R.m.s. deviations | ||||||
| Bond lengths (Å) | 0.005 | 0.005 | 0.005 | - | - | - |
| Bond angles (°) | 1.058 | 1.048 | 1.364 | - | - | - |
| Validation | ||||||
| MolProbity score | 1.69 | 2.07 | 2 | - | - | - |
| Clashscore | 9.18 | 14.77 | 9.26 | - | - | - |
| Poor rotamers (%) | 0.51 | 0.04 | 0 | - | - | - |
| Ramachandran plot | ||||||
| Favored (%) | 96.78 | 94.2 | 91.44 | - | - | - |
| Allowed (%) | 3.22 | 5.8 | 8.04 | - | - | - |
| Disallowed (%) | 0 | 0 | 0.52 | - | - | - |
*
Refers to the number of 96-nm particles.
†
Ranges correspond to the values of the individual maps prior to merging to form the composite map.