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 9U38 | pdb_00009u38

D14.F25.S02 Fab complexed to DENV2-US/BID/V594/2006 virus-3f-2f Fab map


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelSwissModel 
in silico modelAlphaFold 
Sample
dengue virus type 2
Sample Components
Monoclonal antibody D14.F25.S02
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentLEICA EM GP
Cryogen NameETHANE
Sample Vitrification DetailsGP2
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles1559
Reported Resolution (Å)6.48
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryI
Map-Model Fitting and Refinement
Id1
Refinement Space
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
DetailsRigid body fitting has been done using model from high resolution map of similar deposition.
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 Chimera1.17.3
INITIAL EULER ASSIGNMENTcryoSPARC4.6.0
FINAL EULER ASSIGNMENTcryoSPARC4.6.0
CLASSIFICATIONcryoSPARC4.6.0
RECONSTRUCTIONcryoSPARC4.6.0
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION46826