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) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6UWR |
Refinement
RMS Deviations | |
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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 |
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Single heptamer (class 2) of Clostridioides difficile binary toxin translocase CDTb wilt-type after depletion of calcium from RBD1 |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details |
3D Reconstruction | |
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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 | ||||||
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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 | |||||||||
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Detector Type | GATAN K3 (6k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 50 |
Imaging Experiment | 1 |
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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 | ||
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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 | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 1109860 |