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CryoEM reconstruction of integrase filament at the lumen of native HIV-1 cores (box size 34.2 nm)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K6Y experimental model PDB 9C9M experimental model PDB 8A1P experimental model PDB 2B4J experimental model PDB 6SKK
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.969 f_angle_d 0.481 f_chiral_restr 0.04 f_plane_restr 0.004 f_bond_d 0.002
Sample Human immunodeficiency virus 1
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument LEICA PLUNGER Cryogen Name ETHANE-PROPANE Sample Vitrification Details Embedding Material vitreous ice Embedding Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 58103 Reported Resolution (Å) 4.63 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (1K6Y, 9C9M, 8A1P, 2B4J, 6SKK) Refinement Space REAL 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) 49.6
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1500 Maximum Defocus (nm) 3500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 130000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION Topaz PARTICLE SELECTION Gautomatch IMAGE ACQUISITION EPU MODEL FITTING UCSF Chimera INITIAL EULER ASSIGNMENT cryoSPARC 4.6.2 FINAL EULER ASSIGNMENT cryoSPARC 4.6.2 CLASSIFICATION cryoSPARC 4.6.2 RECONSTRUCTION cryoSPARC 4.6.2 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