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Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and INSTI XZ446 (compound 4f)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3L3U experimental model PDB 1K6Y experimental model PDB 5U1C
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 22.423 f_angle_d 0.809 f_chiral_restr 0.054 f_bond_d 0.007 f_plane_restr 0.007
Sample Assembly of HIV integrase and viral DNA
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument HOMEMADE PLUNGER Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 143698 Reported Resolution (Å) 2.8 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C2
Map-Model Fitting and Refinement Id 1 (3L3U, 1K6Y, 5U1C) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Correlation coefficient Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 42
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1500 Maximum Defocus (nm) 3000 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 37000 Calibrated Magnification 63291 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION Warp IMAGE ACQUISITION Leginon CTF CORRECTION Warp MODEL FITTING Coot MODEL REFINEMENT PHENIX 1.16 INITIAL EULER ASSIGNMENT cisTEM 1.0 FINAL EULER ASSIGNMENT cisTEM 1.0 beta CLASSIFICATION cisTEM 1.0 beta RECONSTRUCTION cisTEM 1.0 beta
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 412354