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 9U34 | pdb_00009u34

Helical Reconstruction of DENV2 US/BID-V594/2006 tubular particles bound with D14.F25.S02 fab


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelSwissModel 
in silico modelAlphaFold 
Sample
dengue virus type 2 bound with D14.F25.S02 fab
Sample Components
dengue virus type 2
monoclonal antibody D14.F25.S02
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentLEICA EM GP
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodHELICAL
Number of Particles405
Reported Resolution (Å)14.7
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypeHELICAL
Axial SymmetryC1
Axial Rise11.25
Angular Rotation29.48
Map-Model Fitting and Refinement
Id1
Refinement Space
Refinement ProtocolRIGID BODY FIT
Refinement TargetMap correlation
Overall B Value
Fitting Procedure
Detailscorrelation value= 0.93
Data Acquisition
Detector TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)40
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)1000
Maximum Defocus (nm)2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification81000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION4.0.1
IMAGE ACQUISITIONEPU
CTF CORRECTIONcryoSPARC4.6.0
MODEL FITTINGUCSF Chimera1.18
INITIAL EULER ASSIGNMENTcryoSPARC4.6.0
FINAL EULER ASSIGNMENTcryoSPARC4.6.0
CLASSIFICATIONRELION4.0.1
RECONSTRUCTIONcryoSPARC4.6.0
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION4784