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 3IYO | pdb_00003iyo

Cryo-EM model of virion-sized HEV virion-sized capsid


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ZZQ 
Sample
Hepatitis E capsid
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentHOMEMADE PLUNGER
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles4348
Reported Resolution (Å)10.5
Resolution MethodFSC 0.5 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryI
Map-Model Fitting and Refinement
Id1 (2ZZQ)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Targetcross-correlation
Overall B Value
Fitting Procedure
DetailsREFINEMENT PROTOCOL--Rigid Body DETAILS--Monomer C were divided into Shell and Spike domains and separately fitted by manual docking using program O ...REFINEMENT PROTOCOL--Rigid Body DETAILS--Monomer C were divided into Shell and Spike domains and separately fitted by manual docking using program O and followed by Situs
Data Acquisition
Detector TypeTVIPS TEMCAM-F415 (4k x 4k)
Electron Dose (electrons/Å**2)10
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelJEOL 2100F
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2
Imaging ModeBRIGHT FIELD
Specimen Holder ModelGATAN LIQUID NITROGEN
Nominal Magnification50000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging Details
EM Software
TaskSoftware PackageVersion
MODEL FITTINGSitus
RECONSTRUCTIONP3DR
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
each micrograph