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Structure of a canine circovirus virus-like particle
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5J36
Sample An icosahedral virus-like particle composed of the canine circovirus Cap protein
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details 1 s incubation time, blot time of 2 s, blot force of -2 and no drain time
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 26891 Reported Resolution (Å) 2.26 Resolution Method FSC 0.143 CUT-OFF Other Details Final reconstruction was generated using homogenous refinement in cryoSPARC, and sharpened locally using DeepEMhancer Refinement Type Symmetry Type POINT Point Symmetry I
Map-Model Fitting and Refinement Id 1 (5J36) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Cross-correlation coefficient Overall B Value Fitting Procedure Details ChimeraX was used to perform rigid-body fitting of domains and modelling was performed using Coot and ISOLDE. Refinement was carried out in Phenix.
Data Acquisition Detector Type GATAN K2 QUANTUM (4k x 4k) Electron Dose (electrons/Å**2) 57
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 700 Maximum Defocus (nm) 3500 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 cryoSPARC 4.3.1 IMAGE ACQUISITION EPU 1 CTF CORRECTION cryoSPARC 4.3.1 MODEL FITTING ISOLDE 1.6.0 MODEL FITTING Coot 0.9.8.3 MODEL FITTING UCSF ChimeraX 1.6.1 INITIAL EULER ASSIGNMENT cryoSPARC 4.3.1 FINAL EULER ASSIGNMENT cryoSPARC 4.3.1 CLASSIFICATION cryoSPARC 4.3.1 RECONSTRUCTION cryoSPARC 4.3.1 MODEL REFINEMENT PHENIX 1.20.1_4887
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE Defocus values were estimated using patch CTF estimation, and CTF correction was performed during 3D reconstruction 32271 Blob picking