Table 1 Summary of cryo-EM data collection, processing and analysis.
From: Plant-expressed virus-like particles reveal the intricate maturation process of a eukaryotic virus
Data set | Procapsid | Capsid |
|---|---|---|
Data collection and processing | ||
Microscope | Titan Krios | Titan Krios |
Detector (mode) | Falcon III (integrating) | Falcon III (integrating) |
Magnification | 75,000 × | 75,000 × |
Magnified pixel size (Å) | 1.065 | 1.065 |
Voltage (kV) | 300 | 300 |
Total dose (e−/Å2) | 72.0 | 79.5 |
Defocus range (μm) | −0.7 to −2.7 | −0.8 to −3.0 |
Movies collected | 8554 | 2788 |
Particle images | 5426 | 21,395 |
Symmetry imposed | Icosahedral (I1) | Icosahedral (I1) |
FSC threshold | 0.143 | 0.143 |
Map resolution (Å) | 6.63 | 2.72 |
Map resolution range (Å) | 5.66–13.33 | 2.64–3.77 |
Refinement | ||
Initial model used (PDB code) | 7ANM | 1OHF |
Map sharpening B factor (Å2) | −452.2 | −125.0 |
Model composition (ASU) | Chains A, B, C, D | Chains A, B, C, D |
Non-hydrogen atoms | 17,464 | 17,518 |
Protein residues | 2288 | 2290 |
R.m.s. deviations | ||
Bond lengths (Å) | 0.005 | 0.006 |
Bond angles (°) | 1.02 | 1.04 |
Validation | ||
EMRinger score | N/Aa | 5.1 |
Molprobity score | 2.93 | 1.59 |
Clashscore | 22.45 | 4.06 |
Poor rotamers (%) | 9.68 | 2.08 |
Ramachandran plot: | ||
Favoured (%) | 95.2 | 97.1 |
Allowed (%) | 4.8 | 2.9 |
Disallowed (%) | 0.0 | 0.0 |
Ramachandran Z-score | 1.02 ± 0.02 | 1.36 ± 0.02 |
Fit to map (CCmask) | 0.74 | 0.88 |
Accession codes | ||
EMPIAR (dataset) | 10555 | 10560 |
EMDB (maps) | 11911 | 11830 |
PDB (model) | 7ATA | 7ANM |
