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Cryo-EM structure of the DCAF11 E3 ligase bound to the DDX18 helicase mediated by GSH-M12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-Q8TEB1-F1-v4 experimental model PDB 5FQD in silico model AlphaFold AF-Q9NVP1-F1-v4
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.5225 f_angle_d 0.7367 f_chiral_restr 0.0482 f_plane_restr 0.0104 f_bond_d 0.0035
Sample Ternary complex of the E3 ligase DCAF11 and the helicase DDX18 mediated by GSH-M12
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument LEICA EM GP Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 136583 Reported Resolution (Å) 2.38 Resolution Method FSC 0.143 CUT-OFF Other Details As in cryosparc Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (5FQD) Refinement Space REAL Refinement Protocol OTHER Refinement Target real space correlation Overall B Value Fitting Procedure Details
Data Acquisition Detector Type TFS FALCON 4i (4k x 4k) Electron Dose (electrons/Å**2) 52.004
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 600 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
EM Software Task Software Package Version PARTICLE SELECTION Topaz 0.2.5a MODEL REFINEMENT PHENIX 1.21.2_5419+SVN CTF CORRECTION cryoSPARC 4.5.3 INITIAL EULER ASSIGNMENT cryoSPARC 4.5.3 FINAL EULER ASSIGNMENT cryoSPARC 4.5.3 CLASSIFICATION cryoSPARC 4.5.3 RECONSTRUCTION cryoSPARC 4.6.2
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION As implemented in cryosparc live 3767503 Topaz