7W73

Cryo-EM map of PEDV S protein with one protomer in the D0-up conformation while the other two in the D0-down conformation


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d15.981
f_angle_d0.8244
f_chiral_restr0.055
f_bond_d0.0056
f_plane_restr0.0049
Sample
Intact Porcine epidemic diarrhea virus (strain Pintung 52)
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles9319
Reported Resolution (Å)6.4
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)55.4
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1000
Maximum Defocus (nm)3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification64000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
IMAGE ACQUISITIONEPU
IMAGE ACQUISITIONRELION3.1
IMAGE ACQUISITIONcryoSPARC3.1
CTF CORRECTIONCTFFIND4.1
MODEL FITTINGCoot0.9.4
MODEL REFINEMENTPHENIX1.19.2
INITIAL EULER ASSIGNMENTRELION3.1
FINAL EULER ASSIGNMENTcryoSPARC3.1
RECONSTRUCTIONcryoSPARC3.1
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION337583