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Structure of the native full-length HIV-1 capsid protein A92E in helical assembly (-12,11)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XFX
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.059 f_angle_d 0.807 f_chiral_restr 0.045 f_bond_d 0.012 f_plane_restr 0.005
Sample In vitro assembled HIV-1 capsid in tubular assembly
Specimen Preparation Sample Aggregation State HELICAL ARRAY Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method HELICAL Number of Particles 227844 Reported Resolution (Å) 4.4 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type HELICAL Axial Symmetry C2 Axial Rise 6.95 Angular Rotation -31.13
Map-Model Fitting and Refinement Id 1 (4XFX) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Cross-correlation coefficient Overall B Value 72.14 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 POLARA 300 Minimum Defocus (nm) Maximum Defocus (nm) Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2 Imaging Mode BRIGHT FIELD Specimen Holder Model OTHER Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version CTF CORRECTION RELION 2.0; 3.0 MODEL FITTING Coot MODEL REFINEMENT PHENIX INITIAL EULER ASSIGNMENT RELION 2.0; 3.0 FINAL EULER ASSIGNMENT RELION 2.0; 3.0 CLASSIFICATION RELION 2.0;3.0 RECONSTRUCTION RELION 2.0; 3.0
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION