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Cryo-EM structure of enterohemorrhagic Escherichia coli CdiA-CT:Tu(GTP):Ts:tRNA complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7VMC experimental model PDB 4PC7 in silico model AlphaFold
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 21.7371 f_angle_d 0.6903 f_chiral_restr 0.0496 f_bond_d 0.0089 f_plane_restr 0.0043
Sample Complex of tRNA, Elongation factor Ts, Tu and CDI toxin form Ecoli EC869.
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 264055 Reported Resolution (Å) 2.85 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (7VMC, 4PC7) Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 1800 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 105000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 5.0.6 CTF CORRECTION cryoSPARC 5.0.6 MODEL FITTING UCSF ChimeraX 1.10 INITIAL EULER ASSIGNMENT cryoSPARC 5.0.6 FINAL EULER ASSIGNMENT cryoSPARC 5.0.6 CLASSIFICATION cryoSPARC 5.0.6 RECONSTRUCTION cryoSPARC 5.0.6 MODEL REFINEMENT PHENIX 1.18.2_3874:
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 4014112