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SPA of purified HIV-1 CA protein in vitro assembled with IP6 (mature morphology). 500 uM LEN was added post assembly.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8G6M
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument LEICA EM GP Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 594567 Reported Resolution (Å) 3.5 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C6
Map-Model Fitting and Refinement Id 1 (8G6M) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Cross-correlation coefficient Overall B Value Fitting Procedure Details Molecular dynamics flexible fitting was done using NAMD targeting cross-correlation coefficients.
Data Acquisition Detector Type GATAN K3 BIOCONTINUUM (6k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 400 Maximum Defocus (nm) 2400 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 105000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details Preliminary grid screening was performed manually.
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.3.1 IMAGE ACQUISITION SerialEM 4.1 CTF CORRECTION CTFFIND 4.1.14 MODEL FITTING NAMD 3.0.1 INITIAL EULER ASSIGNMENT cryoSPARC 4.3.1 FINAL EULER ASSIGNMENT RELION 5.0 CLASSIFICATION RELION 5.0 RECONSTRUCTION RELION 5.0 MODEL REFINEMENT NAMD 3.0.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 25118581