Table 1. Statistics of Cryo-EM structures in this study.
| ecPRPS type A filament | ecPRPS type B filament | ecPRPS type AAMP/ADP filament | |
|---|---|---|---|
| (EMD-33305, PDB 7XMU) | (EMD-33309, PDB 7XN3) | (EMD-33306, PDB 7XMV) | |
| Data collection and processing | |||
| EM equipment | Titan Krios | Titan Krios | Titan Krios |
| Detector | K3 camera | K3 camera | K3 camera |
| Magnification | 22,500 x | 22,500 x | 22,500 x |
| Voltage (kV) | 300 | 300 | 300 |
| Electron exposure ((e–/Å2)) | 60 | 60 | 60 |
| Defocus range(μm) | –1.0 to –2.5 | –1.0 to –2.5 | –1.0 to –2.5 |
| Pixel size(Å) | 0.53 | 0.53 | 0.53 |
| Symmetry imposed | D3 | D3 | D3 |
| Number of collected movies | 3,474 | 3,131 | 2,566 |
| Initial particle images (no.) | 887,654 | 1186879 | 1066797 |
| Final particle images (no.) | 70,541 | 168,218 | 53,045 |
| Map resolution (Å) | 2.3 | 2.9 | 2.6 |
| FSC threshold | 0.143 | 0.143 | 0.143 |
| Map resolution range (Å) | 2.3–3.4 | 2.8–4.7 | 2.5–4.6 |
| Refinement | |||
| Initial model used (PDB code) | 4S2U | 4S2U | 4S2U |
| Map sharpening B-factor(Å2) | –45 | –98 | –51 |
| Model composition | |||
| Non-hydrogen atoms | 15,294 | 14,016 | 15,228 |
| Protein residues | 1,842 | 1,830 | 1,842 |
| Ligands | ADP, HSX, PO4, MG | PO4 | AMP, HSX, ADP, MG |
| Waters | 822 | 54 | 810 |
| Ions | 18 | 12 | 12 |
| B factors(Å2) | |||
| Protein | 49 | 65 | 57 |
| Ligand | 55 | 67 | 58 |
| Water | 50 | 57 | 57 |
| R.m.s. deviations | |||
| Bond lengths (Å) | 0.005 | 0.005 | 0.008 |
| Bond angles (°) | 0.736 | 0.609 | 0.800 |
| Validation | |||
| MolProbity score | 1.48 | 2.11 | 1.58 |
| Clashscore | 4.23 | 6.13 | 5.31 |
| Poor rotamers (%) | 1.57 | 2.37 | 1.18 |
| Ramachandran plot | |||
| Favored (%) | 97.36 | 92.08 | 96.37 |
| Allowed (%) | 2.64 | 7.92 | 3.63 |
| Disallowed (%) | 0 | 0 | 0 |