2YEW

Modeling Barmah Forest virus structural proteins

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1SVP
experimental model	PDB	2XFB
experimental model	PDB	2ALA

Sample
BARMAH FOREST VIRUS

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK I
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	5169
Reported Resolution (Å)	5
Resolution Method
Other Details	THE MODELS WERE BUILD USING MODELLER FOR HOMOLOGY -BASED MODELLING AND USING VMD WITH NAMD FOR FLEXIBLE FITTING INTO CRYO-EM DENSITY. CHAIN A DOES NOT CONTAIN RNA-BINDING PART, ABOUT 80 N-TERMINAL RESIDUES. THE STRUCTURE WAS MODELED BASED ON HOMOLOGY TO PROTEIN WITH KNOWN STURUCTURE AND CRYO-EM DENSITY FITTING. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD- 1886. (DEPOSITION ID: 7893).
Refinement Type
Symmetry Type	POINT
Point Symmetry	I

Map-Model Fitting and Refinement
Id	1 (1SVP, 2XFB, 2ALA)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	REFINEMENT PROTOCOL--RIGID BODY

Data Acquisition
Detector Type	GENERIC GATAN
Electron Dose (electrons/Å**2)	20

Imaging Experiment	1
Date of Experiment	2010-01-10
Temperature (Kelvin)	100
Microscope Model	JEOL 3200FSC
Minimum Defocus (nm)	500
Maximum Defocus (nm)	3500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	4.1
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	50000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
MODEL FITTING	UCSF Chimera
RECONSTRUCTION	EMAN
RECONSTRUCTION	MPSA

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	INDIVIDUAL PARTICLES