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CryoEM structure of apo Toxin B (TcdB) from Clostridioides difficile in the open CROP state
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s)
Type
Source
Accession Code
Details
in silico model
AlphaFold
P18177
Sample
Apo Clostridioides difficile Toxin B (TcdB) in the open CROP state
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
351516
Reported Resolution (Å)
3.19
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 ...
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_refine.