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Cryo-EM structure of CRBN-DDB1 in complex with HBS1L and TNG961
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HXB experimental model Other
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.6071 f_angle_d 0.5437 f_chiral_restr 0.0458 f_bond_d 0.0039 f_plane_restr 0.0039
Sample Ternary complex of HBS1L, cereblon, and DDB1 with TNG961
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 669259 Reported Resolution (Å) 2.9 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (5HXB, 5HXB) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target cross-correlation coefficient Overall B Value Fitting Procedure Details rigid body placement of proteins followed by real space refinement
Data Acquisition Detector Type TFS FALCON 4i (4k x 4k) Electron Dose (electrons/Å**2) 48
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 2200 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 130000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION RELION 5.0 IMAGE ACQUISITION RELION 5.0 CTF CORRECTION RELION 5.0 MODEL FITTING PHENIX 1.20.1_4487 CLASSIFICATION RELION 5.0 RECONSTRUCTION RELION 5.0 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 4475226