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An Information Portal to 105025 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
1VYW
  •   Crystallization Hide
    Crystallization Experiments
    pH 7
    Details 20% AMMONIUM SULPHATE, 1M KCL, 40MM HEPES PH 7
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 184.22 α = 90
    b = 184.22 β = 90
    c = 214.72 γ = 120
     
    Space Group
    Space Group Name:    P 62 2 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC
    Collection Date 2003-11-20
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID14-2
    Wavelength 0.934
    Site ESRF
    Beamline ID14-2
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.3
    Resolution(Low) 35
    Number Reflections(Observed) 94577
    Percent Possible(Observed) 99.0
    R Merge I(Observed) 0.081
    B(Isotropic) From Wilson Plot 36.5
    Redundancy 4.8
     
    High Resolution Shell Details
    Resolution(High) 2.3
    Resolution(Low) 2.38
    Percent Possible(All) 97.0
    R Merge I(Observed) 0.69
    Mean I Over Sigma(Observed) 2.3
    Redundancy 4.2
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method OTHER
    reflnsShellList 2.3
    Resolution(Low) 29.86
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 94195
    Number of Reflections(R-Free) 1908
    Percent Reflections(Observed) 99.0
    R-Work 0.229
    R-Free 0.258
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 47.6
    Anisotropic B[1][1] 5.48
    Anisotropic B[1][2] 9.08
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 5.48
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -10.96
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3
    Shell Resolution(Low) 2.44
    Number of Reflections(R-Free) 308
    Number of Reflections(R-Work) 14771
    R-Factor(R-Work) 0.303
    R-Factor(R-Free) 0.328
    R-Free Error 0.019
    Percent Reflections(Observed) 96.5
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_improper_angle_d 0.82
    c_bond_d 0.007
    c_angle_deg 1.2
    c_dihedral_angle_d 20.8
     
    Coordinate Error
    Luzzati ESD(Observed) 0.32
    Luzzati Sigma A(Observed) 0.33
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.36
    Luzzati Sigma A(R-Free Set) 0.34
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 8978
    Nucleic Acid Atoms 0
    Heterogen Atoms 54
    Solvent Atoms 410
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution CNX
    Structure Refinement CNX 2002
     
    Software
    refinement CNX version: 2002
    model building CNX