Table 1 Map and model refinement statistics
From: Integrative structural analysis of Pseudomonas phage DEV reveals a genome ejection motor
Data Collection Statistics | |||||
|---|---|---|---|---|---|
Specimen | Pseudomonas Phage DEV Virion | DEV gp72:gp73 Ejection Proteins | |||
Facility/Microscope | NCEF / Titan Krios | SLAC-Stanford / Titan Krios | |||
Detector | Gatan K3 | Falcon 4 | |||
Imaging Software | SerialEM | EPU | |||
Magnification | 81,000 x | 150,000 x | |||
Voltage (kV) | 300 | 300 | |||
Exposure (e-/Å2) | 50 | 50 | |||
Exposure Time (sec) | 3.2 | 12.9 | |||
Defocus range/step (µm) | -0.8 to -1.6 (0.2 increments) | -0.8 to -2.2 (0.2 increments) | |||
Pixel size (Å) | 1.12 (0.56) | 0.56 (1.12) | |||
Total movies (frames/movie) | 17,245 (40) | 4897 (40) | |||
Total dose (e-/Å2) | 50 | 50 | |||
Refinement Statistics | |||||
|---|---|---|---|---|---|
Entry | Major Capsid protein | Portal Protein/ HT-adapter/ tail tube complex | gp72 pre-ejection conformation | gp53 Long Tail Fiber N-term Barrel | gp72:gp73 post-ejection conformation |
PDB / EMDB entry | 9BGN/ EMD-44518 | 9BGM/ EMD-44517 | 9BGO/ EMD-44519 | 9COD/ EMD-45776 | 8VXQ/ EMD-43629 |
Initial particles number | 109,000 | 310,000 | |||
Final particles number | 19,000 | 16,000 | 16,000 | 8,000 | 61,000 |
Map Resolution (Å) at FSC 0.143 | 3.3 | 3.1 | 4.0 | 4.7 | 3.15 |
Map Symmetry | C5 | C12 | C12 | C15 | C9 |
Initial Model | de novo | de novo | de novo | Alphafold | de novo |
Chains / Residues | 9 / 3,591 | 36 / 13,212 | 12 / 4,740 | 15 / 4,740 | 18 / 4,140 |
Model-to-Map Correlation Coefficient (CC)a | 0.89 | 0.89 | 0.70 | 0.70 | 0.78 |
MolProbity / Clash | 1.7 / 5.1 | 2.0 / 10.9 | 2.0 / 13.2 | 2.0 / 13.2 | 1.6 / 3.2 |
R.M.S. deviations Bond Length (Å) / Angles (°) | 0.002 (1) / 0.6 (15) | 0.007 (0) / 0.7 (46) | 0.002(0) / 0.6(0) | 0.002(0) / 0.6(0) | 0.004(3) / 0.7(23) |
Rotamer outliers (%) | 0.1 | 0.9 | 0.0 | 0.0 | 0.4 |
Ramachandran (%) Fav / Allow / Outlier | 91.5 / 8.4 / 0.1 | 92.2 / 7.6 / 0.2 | 94.6 / 5.4 / 0.0 | 94.6 / 5.4 / 0.0 | 93.2 / 6.7 / 0.1 |
