Table 1 Map and model refinement statistics
From: High-resolution cryo-EM structure of the Pseudomonas bacteriophage E217
Bacteriophage E217 extended tail | Bacteriophage E217 contracted tail | |||||
|---|---|---|---|---|---|---|
Data collection and processing | ||||||
Facility/microscope | NCEF/Titan Krios | NCCAT/Titan Krios | ||||
Camera | Gatan K3 | Gatan K3 | ||||
Magnification | ×81,000 | |||||
Voltage (kV) | 300 | |||||
Electron exposure (e-/Å2) | 50 | |||||
Defocus range (µm) | −0.75 to −1.5 (step 0.25) | |||||
Pixel size (Å) | 1.12 | 1.058 | ||||
Total movies (frames/movie) | 22,015 (40) | 22,714 (40) | ||||
Refinement | ||||||
PDB entry code | 8FRS | 8FVH | 8FUV | 8FVG | 8EON | |
Particles per reconstruction | 13,302 | 15,505 | 13,257 | 10,826 | 10,126 | |
Symmetry | C5 | C6 | C6 | C6 | C3 | |
Model name | capsid: decorating | portal:H-to-T: collar:gateway | extended sheath:tube | contracted sheath | baseplate components | |
Map resolution (Å) | 2.8 | 3.4 | 3.1 | 3.1 | 3.6 | |
FSC threshold | 0.143 | |||||
Initial model used | De novo | De novo | De novo | De novo | De novo + AlphaFold | |
Correlation coefficient (CC) | 0.88 | 0.84 | 0.80 | 0.80 | 0.70 | |
Model composition | ||||||
Number of chains | 14 | 36 | 7 | 13 | 45 | |
Non-hydrogen atoms | 31,497 | 70,392 | 11,202 | 48,022 | 95,688 | |
Residues | 4120 | 8886 | 1500 | 6409 | 12,711 | |
RMS deviations | ||||||
Bond lengths (Å) | 0.002 (0) | 0.003 (0) | 0.003 (0) | 0.003 (0) | 0.009 (21) | |
Bond angles (°) | 0.5 (2) | 0.6 (22) | 0.7 (3) | 0.5 (9) | 0.7 (74) | |
Validation | ||||||
MolProbity score | 1.73 | 1.71 | 2.08 | 1.71 | 2.19 | |
Clashscore | 5.10 | 7.26 | 5.09 | 5.94 | 13.20 | |
Rotamer outliers (%) | 0.00 | 0.07 | 0.00 | 0.04 | 0.02 | |
Ramachandran plot | ||||||
Favored (%) | 92.60 | 95.5 | 93.52 | 94.32 | 89.52 | |
Allowed (%) | 7.1 | 4.3 | 6.3 | 5.6 | 10.1 | |
Outliers (%) | 0.29 | 0.15 | 0.00 | 0.00 | 0.36 | |
