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The ERAD misfolded glycoprotein checkpoint complex from Chaetomium thermophilum (EDEM:PDI heterodimer).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.8999 f_angle_d 0.5102 f_chiral_restr 0.0419 f_plane_restr 0.0047 f_bond_d 0.0024
Sample Complex of Chaetomium thermophilum Endoplasmic reticulum degradation enhancing mannosidase (CtEDEM) and Endoplasmic reticulum degradation enhancing protein disulfide isomerase (CtPDI) Sample Components Chaetomium thermophilum Endoplasmic reticulum degradation enhancing mannosidase (CtEDEM) Endoplasmic reticulum degradation enhancing protein disulfide isomerase (CtPDI)
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details Blotting time 3 s, waiting time 30 s
Sample volume 3 uL, blot force 10
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 1400000 Reported Resolution (Å) 2.6 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 1
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 2500 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 105000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION Topaz IMAGE ACQUISITION EPU MODEL REFINEMENT PHENIX CLASSIFICATION cryoSPARC RECONSTRUCTION cryoSPARC
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION