Table 1 Map and model refinement statistics
From: Structure and function of the yeast amino acid-sensing SEAC–EGOC supercomplex
SEAC–EGOC (EMD-51887) (PDB 9H5K) | SEACwing–EGOC (EMD-51867) (PDB 9H4Q) | |
|---|---|---|
Data collection and processing | ||
Magnification | 165,000 | |
Voltage (kV) | 300 | |
Electron exposure (e− Å−2) | 40 | |
Defocus range (μm) | −1.6 to −0.6 | |
Pixel size (Å) | 0.726 | |
Symmetry imposed | C2 | |
Initial particle images (no.) | 1,649,067 | |
Final particle images (no.) | 208,039 | 133,077 (symmetry expanded) |
Map resolution (Å) | 3.2 | 3.1 |
Fourier shell correlation threshold | 0.143 | 0.143 |
Map resolution range (Å) | 2.207–41.635 | 2.207–43.895 |
Refinement | ||
Initial model used (PDB code) | 8adl, 6jwp | 8ae6 |
Model resolution (Å) | 4.0 | 3.4 |
Fourier shell correlation threshold | 0.5 | 0.5 |
Model composition | ||
Nonhydrogen atoms | 114,312 | 27,485 |
Protein residues | 14,138 | 3,362 |
Nucleotides | 4 | 2 |
Ligands | ZN: 28 | MG: 1 |
MG: 2 | AF3: 1 | |
AF3: 2 | ||
B factors (Å2) | (min/max/mean) | (min/max/mean) |
Protein | 0/688.50/118.99 | 25.45/219.94/81.83 |
Nucleotide | 58.26/112.79/90.99 | 38.04/46.91/42.47 |
Ligand | 71.78/192.70/134.95 | 61.82/78.07/67.87 |
Root mean squared deviations | ||
Bond lengths (Å) | 0.004 | 0.003 |
Bond angles (°) | 0.977 | 0.604 |
Validation | ||
MolProbity score | 1.49 | 1.53 |
Clashscore | 4.27 | 4.39 |
Poor rotamers (%) | 0.00 | 0.00 |
EMRinger score | 1.89 | 2.49 |
Ramachandran plot | ||
Favored (%) | 95.94 | 95.48 |
Allowed (%) | 4.06 | 4.52 |
Disallowed (%) | 0 | 0 |
Ramachandran z score | ||
Whole | −0.98 | −1.00 |
Helix | −0.19 | −0.16 |
Sheet | −0.19 | −0.39 |
Loop | −1.13 | −1.11 |
