3IYW

West Nile virus in complex with Fab fragments of MAb CR4354 (fitted coordinates of envelope proteins and Fab fragments of one icosahedral ASU)


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HG0 
experimental modelPDB 3N9G 
Sample
West Nile virus in complex with Fab fragments of MAb CR4354
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentHOMEMADE PLUNGER
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles5006
Reported Resolution (Å)13.7
Resolution MethodFSC 0.5 CUT-OFF
Other Detailsfinal map includes data to 13.0 Ang resolution (FCS at about 0.2 cut-off) ( Details about the particle: The particles were selected interactively at t ...final map includes data to 13.0 Ang resolution (FCS at about 0.2 cut-off) ( Details about the particle: The particles were selected interactively at the computer terminal. )
Refinement Type
Symmetry TypePOINT
Point SymmetryI
Map-Model Fitting and Refinement
Id1 (2HG0)2 (3N9G)
Refinement SpaceREALREAL
Refinement ProtocolRIGID BODY FITRIGID BODY FIT
Refinement TargetRcritRcrit
Overall B Value
Fitting Procedure
DetailsREFINEMENT PROTOCOL--rigid body DETAILS--For fitting, each E monomer was divided into two rigid bodies, DI+III (residues 1-51, 133-195, and 283-400) ...REFINEMENT PROTOCOL--rigid body DETAILS--For fitting, each E monomer was divided into two rigid bodies, DI+III (residues 1-51, 133-195, and 283-400) and DII (residues other than DI+III).
REFINEMENT PROTOCOL--rigid body DETAILS--The CR4354 was divided into two rigid bodies for fitting, the variable domain (residues L1-L115 and H1-H123, ...REFINEMENT PROTOCOL--rigid body DETAILS--The CR4354 was divided into two rigid bodies for fitting, the variable domain (residues L1-L115 and H1-H123, or residues M1-M115 and K1-K123) and the constant domain (residues L116-L220 and H124-H230, or residues M116-M220 and K124-K230)
Data Acquisition
Detector TypeKODAK SO-163 FILM
Electron Dose (electrons/Å**2)22
Imaging Experiment1
Date of Experiment2009-09-09
Temperature (Kelvin)98
Microscope ModelFEI/PHILIPS CM300FEG/T
Minimum Defocus (nm)1450
Maximum Defocus (nm)3530
Minimum Tilt Angle (degrees)-9999
Maximum Tilt Angle (degrees)-9999
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder ModelGATAN LIQUID NITROGEN
Nominal Magnification45000
Calibrated Magnification47244
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Detailslow dose imaging
EM Software
TaskSoftware PackageVersion
MODEL FITTINGEMfit
RECONSTRUCTIONAuto3DEM
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
Each particle