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Structure of a substrate-bound DQC ubiquitin ligase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LDK experimental model PDB 1X1X
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.807 f_angle_d 0.562 f_chiral_restr 0.038 f_plane_restr 0.003 f_bond_d 0.002
Sample CUL1-SKP1-FBXL17-KEAP1 complex
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE-PROPANE Sample Vitrification Details Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE-PROPANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 160256 Reported Resolution (Å) 8.5 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (1LDK, 1X1X) Refinement Space REAL Refinement Protocol OTHER Refinement Target Overall B Value Fitting Procedure Details Coordinates were fitted as rigid bodies or fragments in Chimera and subsequently geometry-optimized using PHENIX real space refinement.
Data Acquisition Detector Type GATAN K3 (6k x 4k) GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 60 50
Imaging Experiment 1 2 Date of Experiment Temperature (Kelvin) Microscope Model FEI TALOS ARCTICA FEI TALOS ARCTICA Minimum Defocus (nm) 2000 1500 Maximum Defocus (nm) 3000 3000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 2.7 Imaging Mode BRIGHT FIELD BRIGHT FIELD Specimen Holder Model OTHER OTHER Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN FIELD EMISSION GUN Acceleration Voltage (kV) 200 200 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION SerialEM CTF CORRECTION CTFFIND 4 CTF CORRECTION Gctf MODEL FITTING UCSF Chimera IMAGE ACQUISITION SerialEM INITIAL EULER ASSIGNMENT RELION 3 INITIAL EULER ASSIGNMENT cryoSPARC FINAL EULER ASSIGNMENT RELION 3 RECONSTRUCTION RELION 3 MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION As implemented in RELION. 824561 Total number of particles for both datasets. Selected using RELION auto-picking (Laplacian-of-Gaussian).