9MAV | pdb_00009mav

Cryo-EM structure of Dengue virus serotype2 US/BID-V594/2006 strain bound with J9 fab.


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelSwissModel 
in silico modelAlphaFold 
Sample
Dengue virus serotype2 US/BID-V594/2006 strain bound with J9 fab
Sample Components
dengue virus type 2
monoclonal antibody J9
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentLEICA EM GP
Cryogen NameETHANE
Sample Vitrification DetailsGP2
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles2903
Reported Resolution (Å)3.85
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryI
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolBACKBONE TRACE
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)40.3
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
CLASSIFICATIONcryoSPARC4.6.0
RECONSTRUCTIONcryoSPARC4.6.0
MODEL REFINEMENTPHENIX1.21.2_5419
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION15000