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Virus-like Particle based on PVY coat protein with RNA-free helical architecture
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HXX
Sample Virus-like particle from PVY coat protein
Specimen Preparation Sample Aggregation State FILAMENT Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method HELICAL Number of Particles 27500 Reported Resolution (Å) 3.58 Resolution Method FSC 0.143 CUT-OFF Other Details cryoSPARC Helical refinement with initial helical parameters from Ab initio model and helical layer lines Refinement Type Symmetry Type HELICAL Axial Symmetry C1 Axial Rise 5.876 Angular Rotation -48.107
Map-Model Fitting and Refinement Id 1 (6HXX) Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON III (4k x 4k) Electron Dose (electrons/Å**2) 40
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS GLACIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 2100 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 150000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 3.3 CTF CORRECTION cryoSPARC 3.3 MODEL FITTING Coot MODEL REFINEMENT PHENIX INITIAL EULER ASSIGNMENT cryoSPARC 4.1 RECONSTRUCTION cryoSPARC 4.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION patchCTF correction 109796 cryosparc filament tracer