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Poliovirus type 3 (strain Saukett) stabilised virus-like particle (PV3 SC8) from a mammalian expression system.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5O5B
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.2326 f_angle_d 0.4381 f_chiral_restr 0.0403 f_plane_restr 0.0038 f_bond_d 0.0021
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details Double blotting with 4 ul of sample, followed by 4 second blot, before plunging.
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 9630 Reported Resolution (Å) 3 Resolution Method FSC 0.143 CUT-OFF Other Details Final reconstruction was sharpened with Post-processing in RELION using an inverse B-factor of -82.6 Angstroms. Refinement Type Symmetry Type POINT Point Symmetry I
Map-Model Fitting and Refinement Id 1 (5O5B) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Correlation coefficient Overall B Value Fitting Procedure Details Initial model was rigid body fitted using UCSF chimera, and the refined in real space using Phenix_real.space.refine.
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 40
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI POLARA 300 Minimum Defocus (nm) 1500 Maximum Defocus (nm) 3500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model GATAN LIQUID NITROGEN Nominal Magnification 160000 Calibrated Magnification 37037 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION crYOLO 1.5.6 IMAGE ACQUISITION SerialEM CTF CORRECTION CTFFIND 4.0 MODEL FITTING UCSF Chimera 1.14 MODEL REFINEMENT PHENIX dev-3699 INITIAL EULER ASSIGNMENT RELION 3.1 FINAL EULER ASSIGNMENT RELION 3.1 CLASSIFICATION RELION 3.1 RECONSTRUCTION RELION 3.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 14021