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Seneca valley virus Altered particle at acidic condition (A-particle[C])
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CJI
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.473 f_angle_d 0.501 f_chiral_restr 0.042 f_plane_restr 0.005 f_bond_d 0.004
Sample Seneca Valley virus USA/SSV-001
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 817 Reported Resolution (Å) 3.36 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry I
Map-Model Fitting and Refinement Id 1 (3cji, 3cji, 3cji, 3cji) Refinement Space Refinement Protocol AB INITIO MODEL 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 KRIOS Minimum Defocus (nm) 400 Maximum Defocus (nm) 1500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode OTHER Specimen Holder Model Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.5.3 CTF CORRECTION cryoSPARC 4.5.3 MODEL FITTING ISOLDE 1.8 MODEL FITTING UCSF ChimeraX 1.8 MODEL REFINEMENT ISOLDE 1.8 MODEL REFINEMENT Coot 0.9.8.8 MODEL REFINEMENT PHENIX 1.21.2-5419 MODEL REFINEMENT UCSF ChimeraX 1.8 RECONSTRUCTION cryoSPARC 4.5.3
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION