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DDB1-CRBN with Ikaros(ZF2) and DEG-47: composite map and model submission
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8D7Z
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 7.409 f_angle_d 0.571 f_chiral_restr 0.043 f_plane_restr 0.004 f_bond_d 0.002
Sample DDB1(BPB deleted)-CRBN complex with ikaros ZF2-3 and DEG-47 was incubauted for 30 minutes and then plunge frozen over 1.2/1.3 UltrAufoil
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument HOMEMADE PLUNGER Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 412326 Reported Resolution (Å) 2.69 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (8d7z, 8d7z, 8d7z) Refinement Space RECIPROCAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value 97.8 Fitting Procedure Details
Data Acquisition Detector Type TFS FALCON 4i (4k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TALOS ARCTICA Minimum Defocus (nm) 800 Maximum Defocus (nm) 1200 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 19000 Calibrated Magnification 189189 Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.6.2 IMAGE ACQUISITION EPU 3.9.1.8206 CTF CORRECTION cryoSPARC 4.6.2 MODEL FITTING Coot 0.9.8.95 EL (ccp4) INITIAL EULER ASSIGNMENT cryoSPARC 4.6.2 FINAL EULER ASSIGNMENT cryoSPARC 4.6.2 CLASSIFICATION cryoSPARC 4.6.2 RECONSTRUCTION cryoSPARC 4.6.2 MODEL REFINEMENT PHENIX v2.0orc1-5617
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING ONLY 3488921