CryoEM structure of Toxin B (TcdB) from clostridioides difficile complexed with methyl cholate
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 12.9779 |
| f_angle_d | 0.5023 |
| f_chiral_restr | 0.0429 |
| f_plane_restr | 0.0038 |
| f_bond_d | 0.0032 |
| Sample |
|---|
| Clostridioides difficile Toxin B (TcdB) complexed with the synthetic bile acid methyl cholate |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | LEICA EM GP |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | 30s preblot incubation on grid. 2-3s blot time. |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 339310 |
| Reported Resolution (Å) | 2.87 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | OTHER | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | Predicted models were docked into the map using ChimeraX. The model was then manually built with ISOLDE and Coot and refined with phenix.real_space_r ... | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON IV (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 40 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 1000 |
| Maximum Defocus (nm) | 2000 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
| Nominal Magnification | 75000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| IMAGE ACQUISITION | EPU | 3.7 |
| MODEL FITTING | ISOLDE | |
| MODEL FITTING | Coot | 09.8.91 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 4 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 4 |
| CLASSIFICATION | cryoSPARC | 4 |
| RECONSTRUCTION | cryoSPARC | 4 |
| MODEL REFINEMENT | PHENIX | 1.20.1-4487 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||
