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Symmetric structure of Satellite Tobacco Necrosis Virus-Like Particle with PS1-5 gRNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BCU
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 3.687 f_angle_d 0.785 f_chiral_restr 0.053 f_bond_d 0.006 f_plane_restr 0.004
Sample Satellite tobacco necrosis virus 1
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 78988 Reported Resolution (Å) 2.39 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry I
Map-Model Fitting and Refinement Id 1 (4bcu) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Cross-correlation coefficient Overall B Value 129.1 Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 49.5
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 800 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 178000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION RELION 3.0 IMAGE ACQUISITION EPU CTF CORRECTION Gctf 1.06 MODEL FITTING UCSF Chimera 8.6 MODEL REFINEMENT PHENIX 1.9 MODEL REFINEMENT Coot 0.9.6 INITIAL EULER ASSIGNMENT cryoSPARC 3.0 FINAL EULER ASSIGNMENT cryoSPARC 3.0 CLASSIFICATION RELION 3.0 RECONSTRUCTION cryoSPARC 3.0
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 502684