Table 1 Cryo-EM data collection, refinement and validation statistics
From: Structural basis for retron co-option of anti-phage ATPase-nuclease
No. 1 Ec78 4:2:1 (EMDB-49570) (PDB 9NNB) | No. 2 Ec78 4:2:2 (EMDB-49575) (PDB 9NNH) | No. 2 PtuAB (EMDB-49576) (PDB 9NNK) | |
|---|---|---|---|
Data collection and processing | |||
Magnification | ×105,000 | ×105,000 | ×105,000 |
Voltage (kV) | 300 | 300 | 300 |
Electron exposure (e–/Å2) | 50 | 50 | 50 |
Defocus range (μm) | –1.0 to –1.7 | –1.0 to –1.7 | –1.0 to –1.7 |
Pixel size (Å) | 0.828 | 0.828 | 0.828 |
Symmetry imposed | C1 | C1 | C1 |
Initial particle images (no.) | 3,630,467 | 3,630,467 | 6,418,968 |
Final particle images (no.) | 140,378 | 301,183 | 244,056 |
Map resolution (Å) | 2.75 | 2.69 | 3.15 |
FSC threshold | 0.143 | 0.143 | 0.143 |
Map resolution range (Å) | 2.7/3.0/3.2 | 2.7/3.0/3.3 | 3.1/3.3/3.4 |
Refinement | |||
Initial model used (PDB code) | |||
Model resolution (Å) | 2.75 | 2.69 | 3.15 |
FSC threshold | 0.143 | 0.143 | 0.143 |
Model resolution range (Å) | 2.7/2.8/3.2 | 2.6/2.7/3.0 | 3.1/3.1/3.3 |
Map sharpening B factor (Å2) | 98.2 | 87.3 | 118.5 |
Model composition | |||
Non-hydrogen atoms | 25,392 | 29,478 | 21,092 |
Protein residues | 2,863 | 3,243 | 2,622 |
Nucleic acids | 114 | 164 | 0 |
Ligands (ATP) | 3 | 3 | 4 |
B factors (Å2) | |||
Protein | 59.3 | 51.9 | 50.2 |
Nucleic acids | 25.2 | 23.5 | - |
Ligands (ATP) | 36.7 | 17.2 | 14.0 |
R.m.s. deviations | |||
Bond lengths (Å) | 0.007 | 0.005 | 0.007 |
Bond angles (°) | 0.887 | 0.874 | 1.014 |
Validation | |||
MolProbity score | 1.6 | 1.6 | 1.7 |
Clashscore | 5.0 | 4.6 | 4.6 |
Poor rotamers (%) | 0.0 | 0.0 | 0.0 |
Ramachandran plot | |||
Favored (%) | 95.3 | 94.8 | 93.8 |
Allowed (%) | 4.6 | 5.0 | 6.0 |
Disallowed (%) | 0.1 | 0.1 | 0.2 |
