Table 1.
Cryo-EM data collection, processing, and modeling
| Data collection and processing | |||
| Sample | FLAG-VCP (H1299 cells) | His-VCP (E. coli BL21(DE3)), apyrase treated | |
| Microscope | FEI TITAN KROIS | FEI TITAN KROIS | |
| Imaging mode | Microprobe | Microprobe (EF) | |
| Magnification | 22,500 | 105,000 | |
| Voltage (kV) | 300 | 300 | |
| Total dose (e/Å2) | 46 | 40 | |
| Pixel size (Å/pixel) | 0.65 (super) | 0.69 (super) | |
| Frame rate (frames/second) | 5 | 5 | |
| No. of movies | 618 | 807 | |
| 3D classes | dodecamer | hexamer | dodecamer |
| No. of particles | 27,516 | 22,172 | 38,312 |
| Symmetry imposed | D6 | C6 | D6 |
| Map resolution (Å) | 3.9 | 4.2 | 3.7 |
| Map resolution range (Å) | 3.5–12 | 3.5–11 | 3.5–11 |
| FSC threshold | 0.143 | 0.143 | |
| Refinement | |||
| Initial model used | PDB: 5FTN,5FTK | ||
| Map sharpening B factor (Å2) | −143 | −158 | −139 |
| Model composition | |||
| Protein (residues) | 8,892 | 4,446 | 8,892 |
| Nucleotide | 0 | 0 | 0 |
| RMSD from ideal geometry | |||
| Bonds length (Å) | 0.008 | 0.006 | 0.007 |
| Bonds angle (°) | 1.058 | 1.068 | 1.014 |
| Validation | |||
| Molprobity score | 1.85 | 2.00 | 1.73 |
| Clash score | 7.13 | 6.36 | 6.07 |
| Rotamers outliers (%) | 1.10 | 2.19 | 0.94 |
| Ramachandran plot statistics | |||
| Favored (%) | 93.49 | 94.17 | 94.14 |
| Allowed (%) | 6.51 | 5.83 | 5.86 |
| Disallowed (%) | 0 | 0 | 0 |