POP-OUT | CLOSE

An Information Portal to 105339 Biological Macromolecular Structures

ELECTRON MICROSCOPY
Materials and Methods page
1K4R
  •   EM Refinement Details Hide
    3D Reconstruction
    Reconstruction Method COMMON-LINES AND POLAR-FOURIER-TRANSFORM (FULLER ET AL. 1996, J.STRUC.BIOL. 116, 48-55 BAKER AND CHENG, 1996, J.STRUC.BIOL. 116, 120-130) SOFTWARE USED, PURDUE PROGRAMS
     
    EM Map-Model Fitting & Refinement
    Refinement Space REAL
    Fitting Procedure 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.
     
    EM Image Reconstruction Statistics
    Number of Particles 526
    Nominal Pixel Size 2.8
    Actual Pixel Size 2.9
    Effective Resolution 24.0
    CTF Correction Method EACH VIRAL IMAGE WAS CTF CORRECTED BEFORE RECONSTRUCTION, BASED ON THE FOLLOWING EQUATION: F(CORR)=F(OBS)/[|CTF|+WIENER]
     
    Electron Microscope Sample
    Sample pH 7.6
    Sample Support Details sample conc. l2.0E10 PFU/ML
    Sample Vitrification Details LIQUID NITROGEN TEMPERATURE 50MM TRIS-HCL, 75MM NACL, 1MM EDTA
    Sample Aggregation State PARTICLE
    Name of Sample DENGUE VIRUS MAJOR ENVELOPE PROTEIN E
    Sample Details SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE.
     
    Data Acquisition
    Num of Micrographs-Images Used 25
    Temperature (Kelvin) 100.0
    Microscope Model PHILLIPS CM200
    Detector Type KODAK SO163 FILM
    Minimum Defocus (NM) 790.0
    Maximum Defocus (NM) 1920.0
    Minimum Tilt Angle (degrees) 0.0
    Maximum Tilt Angle (degrees) 0.0
    Nominal CS 2.0
    Imaging Mode BRIGHT FIELD
    Electron Dose (electrons nm**-2) 25.5
    Illumination Mode FLOOD BEAM LOW DOSE
    Nominal Magnification 50000
    Source SCHOTTKY FIELD EMISSION GUN
     
    Biomolecule
    COM ID 1
    Name DENGUE VIRUS MAJOR ENVELOPE PROTEIN E
     
    Virus Particulars
    COM ID 1
     
     
  •   Software and Computing Hide
    Computing
    Structure Solution EMFIT
     
    Software
    model building emfit