8EKK
Clostridioides difficile binary toxin translocase CDTb wild-type after calcium depletion from receptor binding domain 1 (RBD1) - Class 2
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 6UWR | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 4.085 |
| f_angle_d | 0.469 |
| f_chiral_restr | 0.043 |
| f_plane_restr | 0.003 |
| f_bond_d | 0.002 |
| Sample |
|---|
| Single heptamer (class 2) of Clostridioides difficile binary toxin translocase CDTb wilt-type after depletion of calcium from RBD1 |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 36395 |
| Reported Resolution (Å) | 3.28 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C7 |
| Map-Model Fitting and Refinement | ||||||
|---|---|---|---|---|---|---|
| Id | Refinement Space | Refinement Protocol | Refinement Target | Overall B Value | Fitting Procedure | Details |
| 1 (6UWR) | AB INITIO MODEL | |||||
| 2 (6UWR) | AB INITIO MODEL | |||||
| 3 (6UWR) | AB INITIO MODEL | |||||
| 4 (6UWR) | AB INITIO MODEL | |||||
| 5 (6UWR) | AB INITIO MODEL | |||||
| 6 (6UWR) | AB INITIO MODEL | |||||
| 7 (6UWR) | AB INITIO MODEL | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 50 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS GLACIOS |
| Minimum Defocus (nm) | 700 |
| Maximum Defocus (nm) | 2500 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.7 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | 45000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 200 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | 3.3.2 |
| IMAGE ACQUISITION | SerialEM | |
| CTF CORRECTION | cryoSPARC | 3.3.2 |
| MODEL FITTING | UCSF Chimera | |
| MODEL REFINEMENT | Coot | |
| MODEL REFINEMENT | PHENIX | |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 3.3.2 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 3.3.2 |
| CLASSIFICATION | cryoSPARC | 3.3.2 |
| RECONSTRUCTION | cryoSPARC | 3.3.2 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 1109860 | |||
