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)
Type	Source	Accession Code	Details
experimental model	PDB	2HG0
experimental model	PDB	3N9G

Sample
West Nile virus in complex with Fab fragments of MAb CR4354

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	HOMEMADE PLUNGER
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	5006
Reported Resolution (Å)	13.7
Resolution Method	FSC 0.5 CUT-OFF
Other Details	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 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 Type	POINT
Point Symmetry	I

Map-Model Fitting and Refinement
Id	1 (2HG0)	2 (3N9G)
Refinement Space	REAL	REAL
Refinement Protocol	RIGID BODY FIT	RIGID BODY FIT
Refinement Target	Rcrit	Rcrit
Overall B Value
Fitting Procedure
Details	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) ...	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 Type	KODAK SO-163 FILM
Electron Dose (electrons/Å**2)	22

Imaging Experiment	1
Date of Experiment	2009-09-09
Temperature (Kelvin)	98
Microscope Model	FEI/PHILIPS CM300FEG/T
Minimum Defocus (nm)	1450
Maximum Defocus (nm)	3530
Minimum Tilt Angle (degrees)	-9999
Maximum Tilt Angle (degrees)	-9999
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	GATAN LIQUID NITROGEN
Nominal Magnification	45000
Calibrated Magnification	47244
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details	low dose imaging

EM Software
Task	Software Package	Version
MODEL FITTING	EMfit
RECONSTRUCTION	Auto3DEM

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	Each particle

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.