☰ Navigation Tabs
De novo designed minibinder complexed with Clostridioides difficile Toxin B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold P18177
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.898 f_angle_d 0.8218 f_chiral_restr 0.0576 f_bond_d 0.0114 f_plane_restr 0.0074
Sample De novo designed minibinder complexed with Clostridioides difficile Toxin B
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 179414 Reported Resolution (Å) 3.02 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 Refinement Protocol OTHER Refinement Target Overall B Value 113 Fitting Procedure Details Predicted models were docked into the map using ChimeraX. The model was then manually with ISOLDE and refined with
phenix.real_space_refine.
Data Acquisition Detector Type FEI FALCON IV (4k x 4k) Electron Dose (electrons/Å**2) 42
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 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