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Structure of the native full-length HIV-1 capsid protein in complex with Cyclophilin A from helical assembly (-13,7)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XFX experimental model PDB 1AK4
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 20.485 f_angle_d 1.064 f_chiral_restr 0.108 f_bond_d 0.012 f_plane_restr 0.006
Sample In vitro assembled HIV-1 capsid in tubular assembly Sample Components HIV-1 capsid Cyclophilin A
Specimen Preparation Sample Aggregation State HELICAL ARRAY Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 136330 Reported Resolution (Å) 4.4 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (4XFX, 1AK4) Refinement Space REAL Refinement Protocol RIGID BODY 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) 40
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) Maximum Defocus (nm) 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 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION SerialEM CTF CORRECTION RELION 2.0; 3.0 MODEL FITTING Coot MODEL FITTING UCSF Chimera INITIAL EULER ASSIGNMENT RELION 2.0; 3.0 FINAL EULER ASSIGNMENT RELION 2.0; 3.0 CLASSIFICATION RELION RECONSTRUCTION RELION 2.0; 3.0 MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION