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Structure of the cargo bound AP-1:Arf1:tetherin-Nef closed trimer monomeric subunit
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4P6Z experimental model PDB 4HMY experimental model PDB 1O3Y experimental model PDB 4EN2
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 8.244 f_angle_d 1.036 f_chiral_restr 0.06 f_bond_d 0.009 f_plane_restr 0.008
Sample Structure of the HIV-Nef tetherin cargo bound AP-1:Arf1 closed trimer monomeric subunit
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 53841 Reported Resolution (Å) 3.73 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (4P6Z, 4HMY, 1O3Y, 4EN2) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Correlation coefficient Overall B Value Fitting Procedure Details Phenix real space refine
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 62.4
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 750 Maximum Defocus (nm) 2000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.6 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 22500 Calibrated Magnification 46849 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION Gautomatch 0.50 IMAGE ACQUISITION SerialEM CTF CORRECTION Gctf 1.06 MODEL FITTING UCSF Chimera 1.12 INITIAL EULER ASSIGNMENT RELION FINAL EULER ASSIGNMENT RELION 2.1 CLASSIFICATION RELION 2.1 RECONSTRUCTION RELION 2.1 MODEL REFINEMENT PHENIX 1.13
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 252212