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Cryo-EM structure of the AGR2 dimer in complex with the monomeric IRE1beta luminal domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-Q76MJ5-F1
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.894 f_angle_d 0.57 f_chiral_restr 0.04 f_plane_restr 0.006 f_bond_d 0.003
Sample The complex of AGR2 and IRE1beta luminal domain
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 313426 Reported Resolution (Å) 2.9 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (9I3F, 9I3F) Refinement Space Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON IV (4k x 4k) Electron Dose (electrons/Å**2) 11.95
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 600 Maximum Defocus (nm) 1800 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version MODEL FITTING UCSF ChimeraX 1.9 INITIAL EULER ASSIGNMENT cryoSPARC 4.6.0 FINAL EULER ASSIGNMENT cryoSPARC 4.6.0 CLASSIFICATION cryoSPARC 4.6.0 RECONSTRUCTION cryoSPARC 4.6.0 MODEL REFINEMENT PHENIX 1.21.2_5419
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION