Table 1 Cryo-EM data collection, refinement, and validation statistics.
T20S-ZYA EMDB-28906 PDB 8F7K | WT T20S EMDB-28878 PDB 8F6A | T20S L81Y EMDB-28876 PDB 8F66 | |
|---|---|---|---|
Data collection and processing | |||
Magnification | ×81,000 | ×81,000 | ×81,000 |
Voltage (kV) | 300 | 300 | 300 |
Electron exposure (e–/Å2) | 50 | 50 | 50 |
Defocus range (μm) | −2.4 to −1.2 | −2.4 to −1.2 | −2.4 to −1.2 |
Pixel size (Å) | 0.54 | 0.54 | 0.54 |
Symmetry imposed | D7 | D7 | D7 |
Initial particle images (no.) | 1,079,760 | 940,560 | 1,352,216 |
Final particle images (no.) | 871,770 | 444,678 | 131,453 |
Map resolution (Å) | 1.94 | 2.06 | 2.28 |
FSC threshold | 0.143 | 0.143 | 0.143 |
Map resolution range (Å) | 1.73–26.10 | 1.86–27.00 | 2.07–30.47 |
Refinement | |||
Initial model used (PDB code) | 1YA7 | 1YA7 | 1YA7 |
Model resolution (Å) | 1.9 | 2.0 | 2.2 |
FSC threshold | 0.143 | 0.143 | 0.143 |
Model composition | |||
Non-hydrogen atoms | 47,264 | 45,948 | 46,508 |
Protein residues | 6048 | 5950 | 6006 |
Ligands | 14 | 0 | 0 |
B factors (Å2) | (min/max/mean) | (min/max/mean) | (min/max/mean) |
Protein | 1.67/78.10/17.90 | 0.95/69.94/13.96 | 1.19/84.10/16.39 |
Ligand | 0.50/0.50/0.50 | ||
R.m.s. deviations | |||
Bond lengths (Å) | 0.005 | 0.004 | 0.005 |
Bond angles (°) | 0.685 | 0.693 | 1.019 |
Validation | |||
MolProbity score | 1.22 | 1.76 | 2.14 |
Clashscore | 3.21 | 4.08 | 6.86 |
Poor rotamers (%) | 1.39 | 3.21 | 3.94 |
Ramachandran plot | |||
Favored (%) | 98.6 | 96.91 | 95.53 |
Allowed (%) | 1.40 | 3.09 | 3.76 |
Disallowed (%) | 0 | 0 | 0.71 |
Ramachandran Z score | |||
Whole | 1.42 | 1.20 | 0.82 |
Helix | 2.03 | 2.27 | 1.33 |
Sheet | 0.83 | 0.48 | 0.72 |
Loop | −0.06 | −0.62 | −0.47 |
