Table 1 Cryo-EM data collection, refinement, and validation statistics
From: Cryo-EM structures of the human Elongator complex at work
ELP123–tRNA–acetyl-CoA (PDB ID 8PTX) (EMD-17924) | ELP123 (PDB ID 8PTY) (EMD-17925) | ELP123–tRNA–ECA (PDB ID 8PTZ) (EMD-17926) | ELP123–tRNA–DCA (PDB ID 8PU0) (EMD-17927) | |
|---|---|---|---|---|
Data collection and processing | ||||
Magnification | 105,000× | 96,000× | 96,000× | 105,000× |
Voltage (kV) | 300 | 300 | 300 | 300 |
Electron exposure (e–/Å2) | 40.84 | 40.00 | 40.00 | 41.22 |
Defocus range (μm) | −0.9 to −2.1 | −0.9 to −2.7 | −0.9 to −2.7 | −0.9 to −2.1 |
Pixel size (Å) | 0.86 | 0.86 | 0.85 | 0.86 |
Symmetry imposed | C1 | C1 | C1 | C1 |
Initial particle images (no.) | 1,250,013 | 264,351 | 130,531 | 699,211 |
Final particle images (no.) | 215,353 | 171,951 | 31,251 | 115,026 |
Map resolution (Å) | 2.87 | 3.58 | 3.35 | 4.25 |
FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 |
Map resolution range (Å) | 1.85 to >10 | 3.30 to 5.50 | 1.82 to >10 | 3.79 to >10 |
Refinement | ||||
Initial model used (PDB code) | ||||
Model resolution (Å) | 1.8 | 3.2 | 2.1 | 3.0 |
FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 |
Map sharpening B factor (Å2) | DeepEMhancer | 120.408 | DeepEMhancer | DeepEMhancer |
Model composition | ||||
Non-hydrogen atoms | 24,378 | 14,189 | 17,194 | 22,416 |
Protein residues | 2852 | 1786 | 1965 | 2612 |
Nucleotides | 75 | – | 75 | 71 |
Ligands | 7 | 2 | 5 | 3 |
Bfactors (Å2) | ||||
Protein | 176.79 | 177.76 | 136.67 | 260.36 |
Nucleotide | 243.32 | – | 251.00 | 243.61 |
Ligand | 118.09 | 182.75 | 121.26 | 258.17 |
R.m.s. deviations | ||||
Bond lengths (Å) | 0.005 | 0.005 | 0.004 | 0.005 |
Bond angles (°) | 0.982 | 0.973 | 0.993 | 0.958 |
Validation | ||||
MolProbity score | 1.70 | 2.09 | 2.05 | 2.33 |
Clashscore | 6.26 | 11.81 | 10.62 | 23.61 |
Poor rotamers (%) | 0.04 | 0.13 | 0.23 | 0.61 |
Ramachandran plot | ||||
Favored (%) | 94.88 | 91.36 | 91.39 | 92.64 |
Allowed (%) | 5.12 | 8.64 | 8.61 | 7.36 |
Disallowed (%) | 0.00 | 0.00 | 0.00 | 0.00 |
