Table 1.
Cryo-EM data collection, refinement and validation statistics.
| GagΔMAT8I assemblies (EMDB-11894) (PDB 7ASH) | GagT8I VLPs (EMDB-11897) (PDB 7ASL) | GagΔMAT8I assemblies + IP6 (EMDB-11899) | |
|---|---|---|---|
| Data acquisition and processing | |||
| EM equipment | Titan Krios | Titan Krios | Titan Krios |
| Detector | Gatan K2 | Gatan K2 | Falcon 4 |
| Energy filter | Gatan GIF Quantum, 20 eV slit | Gatan GIF Quantum, 20 eV slit | Selectris X, 10 eV slit |
| Magnification | 105,000 | 105,000 | 120,000 |
| Voltage (kV) | 300 | 300 | 300 |
| Electron exposure (e-/Å2) | 120 | 110 | 122 |
| Dose rate (e-/Å2/s) | 3 | 3 | 3 |
| Defocus range (μm) | −1.0 ~ −4.0 | −1.5 ~ −3.5 | −1.0 ~ −3.5 |
| Pixel size (Å) | 1.35 | 1.35 | 1.196 |
| Super-resolution mode | Yes | Yes | Yes |
| Symmetry imposed | C6 | C6 | C6 |
| Frame number | 10 | 5 | 10 |
| Acquisition scheme | −60/60°,3° | −54/54°, 3° | −60/60°, 3° |
| Software | SerialEM | SerialEM | TEM Tomography |
| Number of tomograms | 90 | 46 | 13 |
| Initial particle images (no.) | 131,942 | 50,343 | 29,938 |
| Final particle images (no.) | 129,761 | 50,343 | 22,822 |
| Map resolution (Å) | 4.2 | 4.5 | 4.2 |
| FSC threshold | 0.143 | 0.143 | 0.143 |
| Map resolution range (Å) | 4.2–4.5 | 4.4–4.8 | 4.2–4.3 |
| Refinement | |||
| Initial model used (PDB code) | 4XFX, 5L93 | 4XFX, 5L93 | |
| Model resolution (Å) | 4.3 | 4.9 | |
| FSC threshold | 0.3 | 0.3 | |
| Map sharpening B factor (Å2) | −120 | −200 | |
| Model composition | |||
| Non-hydrogen atoms | 0 | 0 | |
| Protein residues | 4194 (18 chains of 233 residues) | 4230 (18 chains of 235 residues) | |
| Ligands | 0 | 0 | |
| R.m.s deviations | |||
| Bond angles (degree) | 1.387 | 2.009 | |
| Bond lengths (Å) | 0.009 | 0.015 | |
| All-atom clash score | 21.39 | 23.92 | |
| Favored rotamers | 100% | 96.97% | |
| Ramachandran plot | |||
| Disallowed (%) | 0 | 0 | |
| Allowed (%) | 2.16% | 3% | |
| Favored (%) | 97.84% | 97% | |
| C-beta deviations | 0.92% | 2.28% | |