Table 1 CryoEM data collection, processing, refinement, and variation statistics
From: Pore formation by the CDTb component of the Clostridioides difficile binary toxin is Ca2+-dependent
| Â | CDTbD623A/D734A | CDTb(-Ca) (Class 1) | CDTb(-Ca) (Class 2) |
|---|---|---|---|
EMDB/PDB | EMDB-28207/8EKM | EMDB-28206/8EKL | EMDB-28205/8EKK |
Data collection and processing | |||
Magnification | 56,240 | 56,240 | 56,240 |
Voltage (kV) | 200 | 200 | 200 |
Electron exposure (e−/Å2) | 45.3 | 59.5 | 59.5 |
Defocus range (μm) | 0.5–2.7 | 0.5–2.7 | 0.5–2.7 |
Pixel size (Ã…) | 0.889 | 0.889 | 0.889 |
Symmetry imposed | C7 | C7 | C7 |
Initial particle images (no.) | 993,305 | 1,109,860 | 1,109,860 |
Final particle images (no.) | 78,587 | 33,531 | 36,395 |
Map resolution (Ã…) | 3.56 | 3.06 | 3.28 |
FSC threshold | 0.143 | 0.143 | 0.143 |
Map resolution range (Å) | 3.56–4.0 | 3.06–4.0 | 3.28–4.0 |
Refinement | |||
Initial model used (PDB code) | 6UWR | 6UWR | 6UWR |
Model resolution (Ã…) | 3.56 | 3.06 | 3.28 |
FSC threshold | 0.143 | 0.143 | 0.143 |
Model resolution range (Å) | 3.56–4.0 | 3.06–4.0 | 3.28–4.0 |
Map sharpening B factor (Å2) | −172.9 | −116.2 | −117.1 |
Model composition | |||
Non-hydrogen atoms | 21,340 | 19,320 | 29,610 |
Protein residues | 2807 | 2485 | 3731 |
Ligands | - | - | - |
B factors (Ã…2) | |||
Protein | 86.7 | 64.9 | 45.79 |
Ligand | - | - | - |
R.m.s. deviations | |||
Bond lengths (Ã…) | 0.013 | 0.003 | 0.003 |
Bond angles (°) | 1.056 | 0.681 | 0.509 |
Validation | |||
MolProbity score | 2.38 | 1.58 | 1.67 |
Clashscore | 12.7 | 5.36 | 6.39 |
Poor rotamers (%) | 0 | 0.32 | 0.27 |
Ramachandran plot | |||
Favored (%) | 77.3% | 95.81 | 95.38 |
Allowed (%) | 22.7% | 4.19 | 4.62 |
Disallowed (%) | 0 | 0 | 0 |
