1K4R | pdb_00001k4r

Structure of Dengue Virus

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1SVB

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	24

Sample
DENGUE VIRUS MAJOR ENVELOPE PROTEIN E

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument
Cryogen Name
Sample Vitrification Details	LIQUID NITROGEN TEMPERATURE 50MM TRIS-HCL, 75MM NACL, 1MM EDTA

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	526
Reported Resolution (Å)	24
Resolution Method
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	I

Map-Model Fitting and Refinement
Id	1 (1SVB)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	METHOD--IN THE FIRST STEP THE CRYSTAL STRUCTURE OF TBEV-E CRYSTALLOGRAPHIC DIMER (REY ET.AL., 1995 NATURELONDON) 375, 291-298) WAS ROTATED ABOUT AND ...	METHOD--IN THE FIRST STEP THE CRYSTAL STRUCTURE OF TBEV-E CRYSTALLOGRAPHIC DIMER (REY ET.AL., 1995 NATURELONDON) 375, 291-298) WAS ROTATED ABOUT AND TRANSLATEDAROUND AN ICOSAHEDRAL TWO FOLD AXES TO FIND THE BEST FIT. AFTER THAT THE DENSITIES AT ALL PIXELS COVERED BY THE FIRST FITTED DIMER WERE SET TO ZERO. THE SECOND DIMER WAS THAN PLACED ON A RADIAL AXIS PASSING THROUGH A POINT NEAR THE QUASI-TWOFOLD AXIS.

Data Acquisition
Detector Type	KODAK SO-163 FILM
Electron Dose (electrons/Å**2)	25.5

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)	100
Microscope Model	FEI/PHILIPS CM200T
Minimum Defocus (nm)	790
Maximum Defocus (nm)	1920
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	50000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)
Imaging Details

EM Software
Task	Software Package	Version
MODEL FITTING	EMfit
RECONSTRUCTION	OTHER

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	EACH VIRAL IMAGE WAS CTF CORRECTED BEFORE RECONSTRUCTION, BASED ON THE FOLLOWING EQUATION: F(CORR)=F(OBS)/[\|CTF\|+WIENER]