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Structure of the immature HTLV-1 CA lattice from full-length Gag VLPs: CA-CTD refinement
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Sample Human T-cell leukemia virus type I
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument LEICA EM GP Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SUBTOMOGRAM AVERAGING Number of Particles 29000 Reported Resolution (Å) 6.2 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C2
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 3.5
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1250 Maximum Defocus (nm) 4000 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 80000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version VOLUME SELECTION subTOM VOLUME SELECTION Warp 1.0.9 VOLUME SELECTION MATLAB R2018b IMAGE ACQUISITION SerialEM CTF CORRECTION Warp 1.0.9 CTF CORRECTION CTFFIND 4.1.10 CTF CORRECTION NOVACTF MODEL FITTING UCSF Chimera FINAL EULER ASSIGNMENT Warp 1.0.9 CLASSIFICATION RELION 3.0.8 RECONSTRUCTION Warp 1.0.9
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION