Table 1 Cryo-EM data collection, refinement and validation statistics
From: Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1
| Â | Structure of substrate bound DRG1 (AFG2) (EMD-14437) (PDB 7Z11) | |
|---|---|---|
Data collection and processing | ||
Magnification | 81,000 | 81,000 |
Voltage (kV) | 300 | 300 |
Electron exposure (e–/Å2) | 60 | 60 |
Defocus range (μm) | −0.5 to −2.5 | −0.5 to −2.5 |
Pixel size (Ã…) | 1.07 | 1.07 |
Symmetry imposed | C1 | C1 |
Initial particle images (no.) | 3,148,330 | 3,645,306 |
Final particle images (no.) | 114,728 | 48,536 |
Map resolution (Ã…) | 3.2 | 4.2 |
 FSC threshold | 0.143 | 0.143 |
Map resolution range (Å) | 4.2–3.2 | 8.5-4.2 |
Refinement | ||
Initial model used (PDB code) | ||
Model resolution (Ã…) | 1.7 | 3.3 |
 FSC threshold | 0.143 | 0.143 |
Model resolution range (Å) | 10–1.7 | 10–3.3 |
Map sharpening B factor (Å2) | −73.2 | −80.4 |
Model composition | ||
 Non-hydrogen atoms | 34,080 | 177,871 |
 Protein residues | 4,404 | 12,625 |
 Nucleotides | - | 3,625 |
 Ligands | AGS: 11 | UNK: 170 MG: 1 AGS: 11 |
B factors (Ã…2) (minimum/maximum/mean) | ||
 Protein | 36.86/137.92/70.04 | 25.24/338.17/138.45 |
 Ligand | 38.86/96.04/55.37 | 32.94/228.74/132.99 |
R.m.s. deviations | ||
 Bond lengths (Å) | 0.004 (0) | 0.002 (0) |
 Bond angles (°) | 0.805 (38) | 0.485 (81) |
Validation | ||
 MolProbity score | 1.89 | 2.49 |
 Clashscore | 8.64 | 16.17 |
 Poor rotamers (%) | 0.35 | 3.4 |
Ramachandran plot | ||
 Favored (%) | 93.60 | 94.46 |
 Allowed (%) | 6.30 | 5.5 |
 Disallowed (%) | 0.09 | 0.03 |
