7Y6S | pdb_00007y6s

Cryo-EM map of IPEC-J2 cell-derived PEDV PT52 S protein with three D0-up

ELECTRON MICROSCOPY

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Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.3222
f_angle_d	0.8274
f_chiral_restr	0.0593
f_bond_d	0.0115
f_plane_restr	0.0045

Sample
recombinat Porcine epidemic diarrhea virus (strain Pintung 52) 2P Spike

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	298195
Reported Resolution (Å)	3.1
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

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		337583