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Cryo-EM map of PEDV (Pintung 52) S protein with all three protomers in the D0-down conformation determined in situ on intact viral particles.
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.805 f_angle_d 0.5839 f_chiral_restr 0.0488 f_bond_d 0.0031 f_plane_restr 0.0029
Sample Intact Porcine epidemic diarrhea virus (strain Pintung 52)
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 19350 Reported Resolution (Å) 4.7 Resolution Method FSC 0.143 CUT-OFF Other Details Non-uniform refinement in CryoSparc3.1 Refinement Type Symmetry Type POINT Point Symmetry C3
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 55.4
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 3000 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 64000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION EPU IMAGE ACQUISITION RELION 3.1 IMAGE ACQUISITION cryoSPARC 3.1 CTF CORRECTION CTFFIND 4.1 MODEL FITTING Coot 0.9.4 MODEL REFINEMENT PHENIX 1.19.2 INITIAL EULER ASSIGNMENT RELION 3.1 FINAL EULER ASSIGNMENT cryoSPARC 3.1 RECONSTRUCTION cryoSPARC 3.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION