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HIV-1 mature capsid pentamer from CA-IP6 CLPs bound to Sec24C peptide
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 12.071 f_angle_d 0.841 f_chiral_restr 0.048 f_plane_restr 0.008 f_bond_d 0.004
Sample HIV-1 Mature Capsid
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 77076 Reported Resolution (Å) 3.14 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C5
Map-Model Fitting and Refinement Id 1 (4XFX) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Cross-correlation Overall B Value Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON IV (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) 600 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 130000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION crYOLO 1.82 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 3.3.2 MODEL FITTING UCSF Chimera INITIAL EULER ASSIGNMENT cryoSPARC 3.3.2 FINAL EULER ASSIGNMENT cryoSPARC 3.3.2 CLASSIFICATION cryoSPARC RECONSTRUCTION cryoSPARC 3.3.2 MODEL REFINEMENT ISOLDE MODEL REFINEMENT Coot MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 2464856