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Cryo-EM structure of DDB1dB-CRBN-MRT-0031619, conformation 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8TNQ
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.436 f_angle_d 0.534 f_chiral_restr 0.044 f_plane_restr 0.004 f_bond_d 0.003
Sample Drug-induced ternary complex between two DDB1-CRBN moieties
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument LEICA EM GP Cryogen Name ETHANE Sample Vitrification Details LEICA EMGP2
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 130145 Reported Resolution (Å) 3.1 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (8TNQ) Refinement Space REAL Refinement Protocol OTHER Refinement Target real space cross correlation Overall B Value 85 Fitting Procedure Details real space refinement in COOT and phenix
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) 800 Maximum Defocus (nm) 2000 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 165000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details collected with AFIS
EM Software Task Software Package Version PARTICLE SELECTION Topaz 0.2.5 IMAGE ACQUISITION EPU 3.8.1 CTF CORRECTION CTFFIND 4.1.10 CTF CORRECTION RELION 5.0 MODEL FITTING UCSF ChimeraX 1.8 MODEL FITTING ISOLDE 1.8 INITIAL EULER ASSIGNMENT RELION 5.0 FINAL EULER ASSIGNMENT RELION 5.0 CLASSIFICATION RELION 5.0 RECONSTRUCTION RELION 5.0 MODEL REFINEMENT PHENIX 1.21
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 4802227 TOPAZ with general model