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Cryo-EM structure of ternary complex BCL6-CRBN-DDB1 with BMS-986458 (local refined), a potent and selective BCL6 ligand directed degrader (LDD)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB PDB_00009Q03
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.724 f_angle_d 0.508 f_chiral_restr 0.041 f_plane_restr 0.005 f_bond_d 0.003
Sample ternary complex of BCL6-CRBN-DDB1 with an LDD BMS-986458
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 202942 Reported Resolution (Å) 3.09 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (pdb_00009q03) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type TFS FALCON 4i (4k x 4k) Electron Dose (electrons/Å**2) 40
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1300 Maximum Defocus (nm) 1900 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 130000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC PARTICLE SELECTION Topaz IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC MODEL FITTING Coot CLASSIFICATION cryoSPARC RECONSTRUCTION cryoSPARC MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 19671274