9MB1 | pdb_00009mb1

Helical Reconstruction of DENV2 THSTI/TRC/01 tubular particles bound with J9 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 J9 fab
Sample Components
dengue virus type 2
monoclonal antibody J9
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodHELICAL
Number of Particles5769
Reported Resolution (Å)14.41
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsResidues involved in atom clashes are the part of immunoglobulin constant region which are appearing to be in head on clash with each other on a dimer ...Residues involved in atom clashes are the part of immunoglobulin constant region which are appearing to be in head on clash with each other on a dimer on which the Fab bind.
Refinement Type
Symmetry TypeHELICAL
Axial SymmetryC1
Axial Rise15.19
Angular Rotation80.62
Axial SymmetryC1
Axial Rise15.19
Angular Rotation80.62
Map-Model Fitting and Refinement
Id1
Refinement Space
Refinement ProtocolRIGID BODY FIT
Refinement Targetmap correlation
Overall B Value
Fitting Procedure
Detailsmap-correlation= 0.8595
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)48
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TALOS ARCTICA
Minimum Defocus (nm)1250
Maximum Defocus (nm)2750
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification36000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION4.0.1
IMAGE ACQUISITIONLatitude
CTF CORRECTIONRELION4.0.1
MODEL FITTINGUCSF Chimera1.17
INITIAL EULER ASSIGNMENTRELION4.0.1
FINAL EULER ASSIGNMENTRELION4.0.1
CLASSIFICATIONRELION4.0.1
RECONSTRUCTIONcryoSPARC4.6.0
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION19729