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An Information Portal to 105339 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3VW3
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 8
    Temperature 277.0
    Details 12% PEG 3350, 0.1M magnesium acetate, 10mM Cobalt hexamine chloride, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 68.43 α = 90
    b = 68.43 β = 90
    c = 243.66 γ = 90
     
    Space Group
    Space Group Name:    P 43 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MAR CCD 165 mm
    Details mirrors
    Collection Date 2002-03-01
     
    Diffraction Radiation
    Monochromator Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SPRING-8 BEAMLINE BL41XU
    Wavelength List 0.8000
    Site SPRING-8
    Beamline BL41XU
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.5
    Resolution(Low) 30
    Number Reflections(Observed) 20541
    Percent Possible(Observed) 97.1
    R Merge I(Observed) 0.054
    B(Isotropic) From Wilson Plot 49.1
    Redundancy 10.5
     
    High Resolution Shell Details
    Resolution(High) 2.5
    Resolution(Low) 2.59
    Percent Possible(All) 97.2
    R Merge I(Observed) 0.24
    Mean I Over Sigma(Observed) 16.0
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.5
    Resolution(Low) 28.26
    Cut-off Sigma(F) 3.0
    Number of Reflections(Observed) 20294
    Number of Reflections(R-Free) 1993
    Percent Reflections(Observed) 96.6
    R-Factor(Observed) 0.247
    R-Work 0.247
    R-Free 0.29
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 54.8
    Anisotropic B[1][1] -7.77
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -7.77
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 15.53
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5
    Shell Resolution(Low) 2.66
    Number of Reflections(R-Free) 322
    Number of Reflections(R-Work) 2916
    R-Factor(R-Work) 0.324
    R-Factor(R-Free) 0.421
    R-Free Error 0.023
    Percent Reflections(Observed) 95.1
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_scangle_it 9.4
    c_scbond_it 7.02
    c_mcangle_it 7.01
    c_mcbond_it 4.86
    c_improper_angle_d 1.12
    c_bond_d 0.009
    c_angle_deg 1.4
    c_dihedral_angle_d 25.6
     
    Coordinate Error
    Luzzati ESD(Observed) 0.35
    Luzzati Sigma A(Observed) 0.26
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.44
    Luzzati Sigma A(R-Free Set) 0.44
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3307
    Nucleic Acid Atoms 732
    Heterogen Atoms 7
    Solvent Atoms 144
     
     
  •   Software and Computing Hide
    Computing
    Data Collection DENZO
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution CNS
    Structure Refinement CNS 1.2
     
    Software
    refinement CNS version: 1.2
    model building CNS
    data collection DENZO