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Cryo-EM structure of porcine epidemic diarrhea virus (PEDV) spike protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5SZS
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.299 f_angle_d 1.626 f_chiral_restr 0.088 f_plane_restr 0.025 f_bond_d 0.017
Sample Porcine epidemic diarrhea virus spike protein
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 19436 Reported Resolution (Å) 3.5 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C3
Map-Model Fitting and Refinement Id 1 (5SZS) Refinement Space REAL Refinement Protocol OTHER Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 54.9
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TECNAI ARCTICA Minimum Defocus (nm) 600 Maximum Defocus (nm) 1400 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION Leginon 3.3 IMAGE ACQUISITION Gctf IMAGE ACQUISITION MotionCorr2 CTF CORRECTION Gctf MODEL FITTING UCSF Chimera 1.13.1 MODEL FITTING Coot 0.9-pre MODEL REFINEMENT Rosetta 3.10 MODEL REFINEMENT PHENIX 1.17rc2-3619 FINAL EULER ASSIGNMENT RELION 3.0 RECONSTRUCTION RELION 3.0
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE 19436