Table 2.
Cryo-EM data collection, refinement, and structure validation
| Data collection | Microtubule–VASH2–SVBP |
|---|---|
| Magnification | 47,260× |
| Pixel size (Å) | 1.058 |
| Defocus range (µm) | −0.6 to −2.2 |
| Voltage (kV) | 300 |
| Exposure time (s per frame) | 0.2 |
| Number of frames | 45 |
| Total dose (e/Å2) | 65 |
| Reconstitution (14 protofilaments microtubules) | |
| Box size (pixels) | 600 |
| Inter-box distance (Å) | 82 |
| Asymmetrical units | 1 |
| Micrographs | 3,345 |
| Picked filaments | 8,987 |
| Initial extracted segments | 153,061 |
| Segments after 3D classification | 97,645 |
| Resolution after 3D auto-refine (Å) | 4.2 |
| Final overall resolution (Å) | 3.2 |
| Estimated map sharpening B-factor (Å2) | −61.03 |
| Helical rise (Å) | 8.99 |
| Helical twist (˚) | -25.73 |
| Reconstitution (single protofilament ) | |
| Particle after expanding 28× | 2,681,616 |
| Particles after 3D classification | 682,072 |
| Occupancy (%) | 50.87 |
| Resolution map:map FSC = 0.143 (Å) | 3.1 (mask: two laterally associated αβ-tubulin heterodimers in complex with VASH2–SVBP) |
| Estimated map sharpening B-factor (Å2) | −112.03 |
| Resolution map:map FSC = 0.143 (Å) | 3.7 (mask: VASH2–SVBP) |
| Atomic model | |
| R.m.s. deviations | |
| Bond lengths (Å) | 0.005 |
| Bond angles (˚) | 0.835 |
| Validation | |
| Map CC (mask) | 0.80 |
| MolProbity clashscore | 3.36 |
| Overall score | 1.42 |
| Rotamer outliers (%) | 0.21 |
| Resolution map:model FSC= 0.5 (Å) | 3.4 |
| Ramachandran plot | |
| Favored (%) | 96.09 |
| Allowed (%) | 3.91 |
| Outliers (%) | 0.00 |