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Structural Insights into HIV-1 Vif-Mediated Ubiquitination and Degradation of APOBEC3H
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4N9Z experimental model PDB 5Z98
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.467 f_angle_d 0.561 f_chiral_restr 0.041 f_plane_restr 0.012 f_bond_d 0.003
Sample Ternary complex of APOBEC3H and Vif of HIV-1
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 294824 Reported Resolution (Å) 3.1 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (4N9Z, 4N9Z, 4N9Z, 4N9Z, 5Z98, 5Z98, 5Z98, 5Z98) Refinement Space Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value 135 Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 45
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TECNAI ARCTICA Minimum Defocus (nm) 800 Maximum Defocus (nm) 2200 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.5.3 IMAGE ACQUISITION EPU 4 CTF CORRECTION cryoSPARC 4.5.3 MODEL FITTING UCSF Chimera 1.6 MODEL REFINEMENT PHENIX 1.21-5207 RECONSTRUCTION cryoSPARC 4.5.3
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING ONLY 7413018