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Cryo-EM structure of KBTBD4 WT-HDAC2-CoREST1 2:1:1 complex mediated by molecular glue UM171
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ZZT in silico model AlphaFold AF-Q9N010-F1
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 9.419 f_angle_d 0.385 f_chiral_restr 0.039 f_plane_restr 0.003 f_bond_d 0.001
Sample KBTBD4 WT-HDAC2-CoREST1 2:1:1 complex mediated by molecular glue UM171
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 105484 Reported Resolution (Å) 3.3 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (7ZZT) Refinement Space Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value 85.1 Fitting Procedure Details Initial local fitting was done using Chimera. Then Coot and Phenix were used for model refinement and validation.
Data Acquisition Detector Type GATAN K3 BIOCONTINUUM (6k x 4k) Electron Dose (electrons/Å**2) 38
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 3200 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 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 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 13588054