Table 2.
Cryo-EM data collection, refinement, and validation statistics
| AnfHDGK (EMD-16890), (PDB 8OIE) | AnfDK (EMD-17583), (PDB 8PBB) | |
|---|---|---|
| Data collection and processing | ||
| Magnification | 105,000 | 105,000 |
| Voltage (kV) | 300 | 300 |
| Electron exposure (e–/Å2) | 50 | 52 |
| Defocus range (μm) | −1.4 to −2.4 | −1.4 to −2.4 |
| Pixel size (Å) | 0.837 | 0.837 |
| Symmetry imposed | C2 | C2 |
| Initial particle images (no.) | 3,014,316 | 7,962,489 |
| Final particle images (no.) | 218,653 | 563,245 |
| Map resolution (Å) | 2.35 | 2.49 |
| FSC threshold | 0.143 | 0.143 |
| Map resolution range (Å) | 1.83–7.30 | 2.21–8.00 |
| Refinement | ||
| Initial model used (PDB code) | 7QAA, AlphaFold39 | AlphaFold39 |
| Model resolution (Å) | 2.34 | 2.48 |
| FSC threshold | 0.143 | 0.143 |
| Model resolution range (Å) | 7.30–2.34 | 8.00–2.48 |
| Map sharpening B factor (Å2) | −50.0 | −107.0 |
| Model composition | ||
| Non-hydrogen atoms | 26,151 | 13,334 |
| Protein residues | 3,262 | 1,648 |
| Ligands | 4 × ADP·AlF3, 4 × Mg2+, 2 × [Fe8S9C], 2 × (R)-homocitrate, 2 × [Fe8S7], 2 × [Fe4S4] | 2 × partial [Fe8S7] |
| B factors (Å2) | ||
| Protein | 61.09 | 29.04 |
| Ligand | 66.10 | 59.13 |
| R.m.s. deviations | ||
| Bond lengths (Å) | 0.012 | 0.006 |
| Bond angles (°) | 0.845 | 0.725 |
| Validation | ||
| MolProbity score | 1.42 | 1.57 |
| Clashscore | 5.12 | 7.38 |
| Poor rotamers (%) | 0.44 | 0.63 |
| Ramachandran plot | ||
| Favored (%) | 97.16 | 97.09 |
| Allowed (%) | 2.84 | 2.91 |
| Disallowed (%) | 0.00 | 0.00 |