Table 1.
Cryo-EM data collection, refinement and validation statistics
| ACAD11 K* 4-HV-CoA (EMD-42954) (PDB 8V3U) |
ACAD11 A* 4-PV-CoA (EMD-42955) (PDB 8V3V) |
|
|---|---|---|
| Data collection and processing | ||
| Magnification | 59k | 59k |
| Voltage (kV) | 300 | 300 |
| Electron exposure (e− Å−2) | 54 | 54 |
| Defocus range (μm) | −1.0 to −2.4 | −1.0 to −2.4 |
| Pixel size (Å) | 1.1 | 1.1 |
| Symmetry imposed | D2 | D2 |
| Initial particle images (number) | 722,751 | 1,294,186 |
| Final particle images (number) | 242,249 | 297,619 |
| Map resolution (Å) | 2.6 | 3.6 |
| FSC threshold | 0.143 | 0.143 |
| Map resolution range (Å) | 2.2–3.0 | 2.5–6.5 |
| Refinement | ||
| Initial model used (PDB code) | AlphaFold and PDB 2WBI | This study and AlphaFold |
| Model resolution (Å) | 2.7 | 3.7 |
| FSC threshold | 0.5 | 0.5 |
| Map sharpening B factor (Å2) | −137.8 | −144.7 |
| Model composition | ||
| Nonhydrogen atoms | 11,928 | 14,468 |
| Protein residues | 1,576 | 2,264 |
| Ligands | 4 | 4 |
| B factors (Å2) | ||
| Protein | 29.19 | 60.32 |
| Ligand | 16.77 | 78.76 |
| R.m.s. deviations | ||
| Bond lengths (Å) | 0.003 | 0.002 |
| Bond angles (°) | 0.461 | 0.447 |
| Validation | ||
| MolProbity score | 1.15 | 1.36 |
| Clash score | 3.55 | 4.66 |
| Poor rotamers (%) | 0.71 | 0.47 |
| Ramachandran plot | ||
| Favored (%) | 98.97 | 97.36 |
| Allowed (%) | 1.03 | 2.64 |
| Disallowed (%) | 0 | 0 |