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Cryo-EM structure of human full-length XPO1 (unliganded)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GB8
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 3.5521 f_angle_d 0.4644 f_chiral_restr 0.0348 f_plane_restr 0.0033 f_bond_d 0.0023
Sample Human full-length unliganded exportin-1 (XPO1)
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 365756 Reported Resolution (Å) 2.93 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (3GB8) Refinement Space REAL Refinement Protocol OTHER Refinement Target Overall B Value 124.05 Fitting Procedure Details Initial model was docked into maps using UCSF ChimeraX then manually built using Isolde and Coot and refined in PHENIX
Data Acquisition Detector Type FEI FALCON IV (4k x 4k) Electron Dose (electrons/Å**2) 60
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 900 Maximum Defocus (nm) 2200 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 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 cryoSPARC PARTICLE SELECTION Topaz IMAGE ACQUISITION SerialEM CTF CORRECTION cryoSPARC MODEL FITTING UCSF ChimeraX MODEL FITTING ISOLDE MODEL FITTING Coot INITIAL EULER ASSIGNMENT cryoSPARC FINAL EULER ASSIGNMENT cryoSPARC CLASSIFICATION cryoSPARC RECONSTRUCTION cryoSPARC MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 1245354 blob picking followed by Topaz picking