Table 1.
Cryo-EM data collection, refinement and validation statistics
| PaaZ (EMDB-9873) (PDB 6JQL) | PaaZ + NADPH (EMDB-9874) (PDB 6JQM) | PaaZ + NADP+ + OcoA (EMDB-9875) (PDB 6JQN) | PaaZ + NADP+ + CCoA (EMDB-9876) (PDB 6JQO) | |
|---|---|---|---|---|
| Data collection and processing | ||||
| Magnification | 75,000 | 75,000 | 75,000 | 75,000 |
| Voltage (kV) | 300 | 300 | 300 | 300 |
| Electron exposure (e−/Å2) | 27 | 27 | 27 | 27 |
| Defocus range (μm) | 2.2–3.2 | 2.2–3.2 | 2.2–3.2 | 2.2–3.2 |
| Pixel size (Å) | 1.06 | 1.06 | 1.06 | 1.04 |
| Symmetry imposed | C3 | C3 | C3 | C3 |
| Initial particle images (no.) | 118,203 | 175,448 | 179,312 | 122,876 |
| Final particle images (no.) | 86,420 | 103,298 | 101,503 | 120,968 |
| Map resolution (Å) | 2.9 | 3.3 | 3.1 | 3.1 |
| FSC threshold (0.143)a | ||||
| Map resolution range (Å)b | 2.5–8 | 2.5–8 | 2.5–8 | 2.5–8 |
| Refinement | ||||
| Initial model used (PDB code) | — | — | — | — |
| Model resolution (Å) | 3.5 | 3.7 | 3.5 | 3.5 |
| FSC threshold (0.5)a | ||||
| Model resolution range (Å) | 436–2.9 | 436–3.3 | 436–3.1 | 428–3.1 |
| Map sharpening B factor (Å2) | 98 | 140 | 120 | 102 |
| Model composition | ||||
| Non-hydrogen atoms | 30,648 | 30,936 | 31,278 | 31,254 |
| Protein residues | 4068 | 4068 | 4068 | 4068 |
| Ligands | — | 6 | 12 | 12 |
| B factors (Å2) | ||||
| Protein | 44.4 | 69 | 60 | 44.2 |
| NADP+/NAPDH | — | 76.5 | 63.7 | 45.8 |
| OCoA/CCoA | — | — | 53.2 | 68.9 |
| R.m.s. deviations | ||||
| Bond lengths (Å) | 0.005 | 0.006 | 0.007 | 0.006 |
| Bond angles (°) | 1.2 | 1.2 | 1.2 | 1.2 |
| Validation | ||||
| MolProbity score | 1.7 | 1.7 | 1.7 | 1.7 |
| Clashscore | 6.8 | 5.8 | 5.7 | 5.7 |
| Poor rotamers (%) | 0.16 | 0.06 | 0 | 0.13 |
| Ramachandran plot | ||||
| Favored (%) | 95.2 | 94.2 | 94.0 | 94.6 |
| Allowed (%) | 4.8 | 5.8 | 6 | 5.4 |
| Disallowed (%) | 0 | 0 | 0 | 0 |
aThe Fourier Shell correlation (FSC) value is between two half-maps of the data (@0.143) and the refined model and combined map (@0.5). bfrom resmap