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Ternary structure of intramolecular bivalent glue degrader IBG1 bound to BRD4 and DCAF16:DDB1deltaBPB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FQD experimental model PDB 3MXF experimental model PDB 6DUV other Other
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.9386 f_angle_d 0.5047 f_chiral_restr 0.0418 f_plane_restr 0.0042 f_bond_d 0.0025
Sample Ternary complex of bivalent glue degrader compound 1 bound to BRD4 and DCAF16:DDB1deltaBPB Sample Components DCAF16:DDB1deltaBPB E3 ligase substrate receptor:apator complex
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details 3.5 uL complex was dispensed onto the grid, allowed to disperse for 10 s, blotted for 3.5 s using blot force 3, then plunged into liquid ethane
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 192014 Reported Resolution (Å) 3.77 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (5FQD, 3MXF, 6DUV) Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type TFS FALCON 4i (4k x 4x) Electron Dose (electrons/Å**2) 12.7
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS GLACIOS Minimum Defocus (nm) 1700 Maximum Defocus (nm) 3200 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 190000 Calibrated Magnification 190000 Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.1.2 IMAGE ACQUISITION EPU 3.0 CTF CORRECTION cryoSPARC 4.1.2 MODEL FITTING PHENIX 1.20.1-4487 INITIAL EULER ASSIGNMENT cryoSPARC 4.1.2 FINAL EULER ASSIGNMENT cryoSPARC 4.2.1 RECONSTRUCTION cryoSPARC MODEL REFINEMENT PHENIX 1.20.1-4487 MODEL REFINEMENT UCSF ChimeraX 1.6.dev202302040126 MODEL REFINEMENT ISOLDE 1.6.dev1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION