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Ternary complex of an improved charged molecular glue degrader ZZ2-SO2H, BRD4(BD1) neosubstrate, and the CTLH E3 ligase receptor module YPEL5-WDR26
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9GHQ
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.497 f_angle_d 0.545 f_chiral_restr 0.044 f_bond_d 0.003 f_plane_restr 0.003
Sample ZZ2-SO2H-induced complex between YPEL5-CTLH E3 ligase and the first bromodomain (BD1) of BRD4
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument Cryogen Name NITROGEN Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 24545 Reported Resolution (Å) 3.42 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (9GHQ) 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) 63.6
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 2300 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION Gautomatch MODEL REFINEMENT PHENIX 1.21.1_5286 RECONSTRUCTION RELION
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 5422892