Table 1 Cryo-EM data collection, refinement and validation statistics
From: Structures of KEOPS bound to tRNA reveal functional roles of the kinase Bud32
| Â | Apo KEOPS | KEOPS + tRNA (native-like conformation) | KEOPS + tRNA (distorted conf ormation) |
|---|---|---|---|
PDB ID | 8UNK | 8UP5 | 9D85 |
EMDB ID | EMD-43407 | EMD-42443 | EMD-46630 |
Data Collection and Processing | |||
Magnification | 105 000 | 105 000 | 105 000 |
Voltage (kV) | 300 | 300 | 300 |
Electron exposure (e-/ Ã…2) | 55.61 | 55.61 | 55.61 |
Defocus range- tilted (μm) | -3.4 to -6.1 | -3.4 to -6.1 | -3.4 to -6.1 |
Defocus range- non tilted (μm) | -0.4 to -2.9 | -0.4 to -2.9 | -0.4 to -2.9 |
Pixel size (Ã…) | 0.825 | 1.03 | 1.03 |
Symmetry imposed | C1 | C1 | C1 |
Final particle images (no.) | 386 585 | 121 003 | 83,710 |
Map resolution (Ã…) | 2.91 | 3.56 | 3.59 |
FSC threshold | 0.143 | 0.143 | 0.143 |
Refinement | |||
Initial model used (PDB codes) | 3ENH/3ENO | 3ENH/3ENO/7KJT | 3ENH/3ENO/7KJT |
Model resolution (Ã…) | 3.1 | 3.5 | 3.5 |
FSC threshold | 0.143 | 0.143 | 0.143 |
Map sharpening B factor (Ã…2) | 133.5 | 147.1 | 150.18 |
Model composition | |||
Non-hydrogen atoms | 9 865 | 6810 | 7201 |
Protein residues | 691 | 712 | 739 |
Nucleotide | 0 | 73 | 65 |
Ligands | 0 | 0 | 0 |
R.m.s. deviations | |||
Bond lengths (Ã…) | 0.003 | 0.004 | 0.005 |
Bond angles (°) | 0.55 | 0.97 | 1.344 |
Validation | |||
MolProbity score | 2.19 | 2.3 | 2.35 |
Clashscore | 22.66 | 24.48 | 27.16 |
Poor rotamers (%) | 0 | 0.6 | 0.33 |
Ramachandran plot | |||
Favored (%) | 95.1 | 93.66 | 93.43 |
Allowed (%) | 4.9 | 6.34 | 6.43 |
Disallowed (%) | 0 | 0 | 0.14 |
