Table 2.
Cryo-EM data collection, refinement, and validation statistics.
| (EMDB/PDB ID) | TlCPC-6 (EMD-31090/7EH8) | TlCPC-8 (EMD-31089/7EH7) |
|---|---|---|
| Data collection and processing | ||
| Microscope | Talos Arctica | Talos Arctica |
| Voltage (kV) | 200 | 200 |
| Detector | Falcon 3EC | Falcon 3EC |
| Magnification | 120,000 | 120,000 |
| Pixel size (Å) | 0.88 | 0.88 |
| Automation software | EPU | EPU |
| Total exposure (e–/Å2) | 50 | 50 |
| Exposure rate (e–/Å2 fraction) | 1.02 | 1.02 |
| Number of frames | 49 | 49 |
| Defocus range (μm) | −1, −1.5, −2, −2.5 | −1, −1.5, −2, −2.5 |
| Number of collected micrograph | 2,036 | 2,036 |
| Number of particles for Class2D | 283,980 | 129,653 |
| Number of particles for Class3D | 72,655 | 23,643 |
| Number of particles for Refine3D | 28,120 | 10,402 |
| Symmetry imposed | D3 | D4 |
| Map resolution (Å) | 3.06 | 3.71 |
| FSC threshold | 0.143 | 0.143 |
| Map resolution range (Å) | 2.91–3.38 | 3.47–4.49 |
| Refinement | ||
| Refinement programs | PHENIX/Coot | PHENIX/Coot |
| Initial model used (PDB code) | 7EFW | 7EFV |
| Map-to-model resolution (Å) | 3.05 | 3.75 |
| FSC threshold | 0.5 | 0.5 |
| Model resolution range (Å) | 2.91–3.38 | 3.47–4.49 |
| Model composition | ||
| Non-hydrogen atoms | 15773 | 20904 |
| Protein residues | 2004 | 2656 |
| Ligands | 18 | 24 |
| B factors (Å2) | ||
| Protein | 38.8 | 51.9 |
| Ligand | 39.4 | 51.2 |
| Map-model CC | ||
| CC (mask) | 0.90 | 0.86 |
| CC (box) | 0.77 | 0.80 |
| CC (peaks) | 0.75 | 0.75 |
| CC (volume) | 0.85 | 0.83 |
| R.m.s. deviations | ||
| Bond lengths (Å) | 0.003 | 0.004 |
| Bond angles (°) | 1.051 | 1.298 |
| Validation | ||
| MolProbity score | 1.3 | 1.7 |
| Clash score | 5.5 | 8.7 |
| Poor rotamer (%) | 0.79 | 1.69 |
| Ramachandran plot | ||
| Favored (%) | 98.2 | 97.8 |
| Allowed (%) | 1.8 | 2.2 |
| Disallowed (%) | 0 | 0 |