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. 2023 Jan 9;51(5):2011–2032. doi: 10.1093/nar/gkac1232

Table 1.

Cryo-EM data collection, refinement and validation statistics

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