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An Information Portal to 105212 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
1SKM
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.5
    Temperature 289.0
    Details PEG 6000, sodium cacodylate, magnesium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 95.68 α = 90
    b = 95.68 β = 90
    c = 315.68 γ = 120
     
    Space Group
    Space Group Name:    H 3 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 4
    Collection Date 2001-10-20
     
    Diffraction Radiation
    Monochromator Si 111 CHANNEL
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X26C
    Wavelength List 1.1
    Site NSLS
    Beamline X26C
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.2
    Resolution(Low) 24.53
    Number Reflections(All) 24477
    Number Reflections(Observed) 23477
    Percent Possible(Observed) 81.9
    B(Isotropic) From Wilson Plot 13.5
    Redundancy 2.9
     
    High Resolution Shell Details
    Resolution(High) 2.2
    Resolution(Low) 2.25
    Percent Possible(All) 36.9
    R Merge I(Observed) 0.179
    Number Unique Reflections(All) 689
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.2
    Resolution(Low) 24.53
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 23477
    Number of Reflections(Observed) 23477
    Number of Reflections(R-Free) 1134
    Percent Reflections(Observed) 81.9
    R-Factor(Observed) 0.183
    R-Work 0.183
    R-Free 0.221
    R-Free Selection Details random
     
    Temperature Factor Modeling
    Isotropic Thermal Model Anisotropic
    Anisotropic B[1][1] 0.74
    Anisotropic B[1][2] 1.85
    Anisotropic B[1][3] -2.58
    Anisotropic B[2][2] 2.3
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.0
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2
    Shell Resolution(Low) 2.25
    Number of Reflections(R-Free) 22
    R-Factor(R-Work) 0.261
    R-Factor(R-Free) 0.303
    R-Free Error 0.065
    Percent Reflections(Observed) 34.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    IMPROPER ANGLES 1.6
    DIHEDRAL ANGLES 22.4
    Bond Angles 1.2
    Bond Lengths 0.007
     
    Coordinate Error
    Luzzati ESD(Observed) 0.24
    Luzzati Sigma A(Observed) 0.23
    Luzzati Resolution Cutoff(Low) 25.0
    Luzzati ESD(R-Free Set) 0.29
    Luzzati Sigma A(R-Free Set) 0.26
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2591
    Nucleic Acid Atoms 499
    Heterogen Atoms 26
    Solvent Atoms 257
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) CAD4
    Data Reduction (data scaling) SCALEPACK
    Structure Solution GLRF
    Structure Refinement CNS
     
    Software
    refinement CNS
    model building GLRF
    data reduction SCALEPACK
    data collection CAD4