Table 1.
ScElongator EMD-15622 PDB ID 8ASV |
ScElp456 EMD-15635 PDB ID 8AT6 |
ScElp123–tRNA EMD-15623 PDB ID 8ASW |
MmElp123 EMD-15682 PDB ID 8AVG |
MmElp123–tRNA EMD-15625 | MmElongator EMD-15626 | |
---|---|---|---|---|---|---|
Data collection and processing | ||||||
Magnification | 105 000× | 81 000× | 165 000× | 105 000× | 105 000× | 105 000× |
Voltage (keV) | 300 | 300 | 300 | 300 | 300 | 300 |
Electron exposure (e-/Å2) | 40 | 40 | 42.45 | 40 | 40 | 40 |
Defocus range | −0.9 to −3.0 | −0.9 to −3.0 | −0.8 to −2.0 | −0.9 to −3.0 | −0.9 to −1.5 | −0.9 to −3.0 |
Pixel size (Å) | 0.86 | 1.1 | 0.81 | 0.86 | 0.86 | 0.86 |
Symmetry imposed | C1 | C1 | C1 | C1 | C1 | C1 |
Initial particle images (no.) | 188 389 | 364 424 | 693 585 | 364 424 | 161 871 | 581 666 |
Final particle images (no.) | 12 514 | 128 593 | 16 809 | 42 894 | 24 829 | 27 128 |
Map resolution (Å) | 4.35 | 3.7 | 3.96 | 4.01 | 4.35 | 5.9 |
FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
Map resolution range (Å) | 3.9 to >10 | 3.6 to 6.6 | 3.7 to 9.7 | 3.8 to >10 | 2.8 to >10 | 4.4 to >10 |
Refinement | ||||||
Initial model used | 6QK7 and 4A8J | 4A8J | 6QK7 | 6QK7 | ||
Model resolution (Å) | 3.5 | 3.7 | 3.5 | 3.5 | ||
FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | ||
Model resolution range (Å) | n/a | n/a | n/a | n/a | ||
Map sharpening B factor (Å2) | −141.69 | −129.16 | −67.83 | −131.78 | ||
Model composition | ||||||
Non-hydrogen atoms | 35 795 | 12 587 | 24 783 | 13 749 | ||
Protein residues | 4478 | 1580 | 2897 | 1732 | ||
Nucleotide residues | 73 | |||||
Ligands | 1 | 0 | 2 | 2 | ||
B factors (Å2) | ||||||
Protein | 99.05 | 107.76 | 97.38 | 84.42 | ||
Nucleotide | 254.23 | |||||
Ligands | 60.85 | 61.57 | 55.04 | |||
R.m.s. deviations | ||||||
Bond lengths (Å) | 0.004 | 0.004 | 0.006 | 0.004 | ||
Bond angles (°) | 0.990 | 0.974 | 1.014 | 0.989 | ||
Validation | ||||||
MolProbity score | 2.13 | 1.92 | 2.35 | 2.17 | ||
Clashscore | 12.59 | 9.75 | 19.37 | 13.21 | ||
Poor rotamers (%) | 0.02 | 0.00 | 0.71 | 0.07 | ||
Ramachandran | ||||||
Favored (%) | 90.93 | 93.80 | 89.25 | 90.48 | ||
Allowed (%) | 9.00 | 5.88 | 10.51 | 9.34 | ||
Disallowed (%) | 0.07 | 0.32 | 0.24 | 0.18 | ||
CC volume | 0.65 | 0.85 | 0.76 | 0.71 |