Table 1.
Data Acquisition, Processing and Model Refinement.
| Data acquisition & processing parameters | ∆pih1-90S |
|---|---|
| Microscope | Titan Krios |
| Detector | Gatan K3 |
| Voltage | 300 kV |
| Electron source | Field Emission Gun |
| Collecting mode | Super-resolution |
| Dose Rate (e-/Å2) | 40 |
| Defocus range (μm) | −1.3 to −2.5 |
| Nominal magnification | 81,000X |
| Frames collected per exposure | 50 |
| Energy filter | 20 eV |
| Framealingment software | MotionCor2 |
| CTF parameter estimation | Gctf |
| Total number of raw images collected | 4644 |
| Number of images used for particle picking | 3477 |
| Initial particles picked | 233,968 |
| 2D classification software | Relion 3.1 |
| Final reconstruction software | Relion 3.1 |
| Applied symmetry | C1 |
| Number of particles contributed for the final reconstruction | 199,534 (Overall and central domain) |
| 84,570 (Head domain) | |
| Resolution method | FSC 0.143 cut-off |
| Map resolution (Å) | 3.99 Å (Overall) |
| 5.04 Å (Head) | |
| 7.24 Å (Central) | |
| Local resolution determining software | Resmap |
| Map visualization software | Pymol/Chimera/Chimera X/ Coot |
| Deposit EMDB codes | 25,441 |
| Refinement parameters | |
| CC (map_model) | 0.77 (mask), 0.77 (volume), 0.83 (box) |
| RMSD (Bond lengths/Bond angles) | 0.008/0.719 |
| Ramachandran plot (%) (Outlier/Allowed/Favored) | (0.03/8.57/91.40) |
| Cβ Outliers (%) | 0.00 |
| MolProbity score | 2.58 |
| Clash score | 39.08 |
| Rotamer outliers (%) | 0.18 |
| ADP (B-factor) (Å2) | 213241 |
| Protein (min/max/mean) | 28.46/292.48/95.52 |
| Nucleotide (min/max/mean) | 45.90/488.62/166.35 |
| Ligand (min/max/mean) | 55.90/172.44/108.55 |
| dFSC model (0.5) | 4.00 |
| Deposit PDB codes | 7SUK |