Table 1 Cryo-EM data collection, refinement, and validation statistics
From: Structural basis of Spliced Leader RNA recognition by the Trypanosoma brucei cap-binding complex
TbCBC-tetramer EMD-50173 PDB-9F3F | TbCBC-trimer EMD-50217 PDB-9F67 | |
|---|---|---|
Data collection and processing | ||
Magnification | 165 000 | 105 000 |
Voltage (kV) | 300 | 300 |
Electron exposure (e–/Å2) | 51.56 | 37.8 |
Defocus range (μm) | − 1 to − 2.4 | − 1 to − 2.4 |
Pixel size (Å) | 0.8127 | 0.42 |
Symmetry imposed | C1 | C1 |
Initial particle images (no.) | 6,907,011 | 3,042,614 |
Final particle images (no.) | 251,312 | 69,764 |
Map resolution (Å) | 2.4 | 2.8 |
FSC threshold | 0.143 | 0.143 |
Refinement | ||
Initial model used (PDB code) | – | 9F3F |
Map sharpening B factor (Å2) | − 42.6 | − 90.0 |
Model composition | ||
Non-hydrogen atoms | 7505 | 7948 |
Protein residues | 939 | 981 |
Ligands | 1 | 1 |
B factors (Å2) | ||
Protein | 48.67 | 61.58 |
Ligand | 65.23 | 135.2 |
R.m.s. deviations | ||
Bond lengths (Å) | 0.008 | 0.009 |
Bond angles (°) | 1.353 | 1.356 |
Validation | ||
MolProbity score | 2.31 | 1.93 |
Clashscore | 16.31 | 13.35 |
Rotamer outliers (%) | 2.45 | 0.12 |
Ramachandran plot | ||
Favored (%) | 95.67 | 95.77 |
Allowed (%) | 4.33 | 4.23 |
Disallowed (%) | 0 | 0 |
