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An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
2WDK
  •   Crystallization Hide
    Crystallization Experiments
    pH 7.1
    Details pH 7.1
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 210.86 α = 90
    b = 450.46 β = 90
    c = 628.88 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 77
     
    Diffraction Detector
    Detector PIXEL
    Type PSI PILATUS 6M
    Collection Date 2008-07-20
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SLS BEAMLINE X06SA
    Wavelength 1.000
    Site SLS
    Beamline X06SA
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 1.0
    Resolution(High) 3.4
    Resolution(Low) 50
    Number Reflections(Observed) 789136
    Percent Possible(Observed) 97.1
    R Merge I(Observed) 0.2
    B(Isotropic) From Wilson Plot 52.0
    Redundancy 5.6
     
    High Resolution Shell Details
    Resolution(High) 3.4
    Resolution(Low) 3.5
    Percent Possible(All) 75.0
    R Merge I(Observed) 0.97
    Mean I Over Sigma(Observed) 1.04
    Redundancy 2.48
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 3.5
    Resolution(Low) 50.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 738740
    Number of Reflections(R-Free) 33747
    Percent Reflections(Observed) 99.1
    R-Factor(Observed) 0.208
    R-Work 0.208
    R-Free 0.256
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 105.9
    Anisotropic B[1][1] 1.64
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -6.29
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 4.64
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5
    Shell Resolution(Low) 3.72
    Number of Reflections(R-Free) 5890
    Number of Reflections(R-Work) 113302
    R-Factor(R-Work) 0.32
    R-Factor(R-Free) 0.35
    R-Free Error 0.005
    Percent Reflections(Observed) 96.6
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_improper_angle_d 1.5
    c_bond_d 0.007
    c_angle_deg 1.5
    c_dihedral_angle_d 28.9
     
    Coordinate Error
    Luzzati ESD(Observed) 0.43
    Luzzati Sigma A(Observed) 0.74
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.5
    Luzzati Sigma A(R-Free Set) 0.81
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 19157
    Nucleic Acid Atoms 37435
    Heterogen Atoms 718
    Solvent Atoms 0
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XDS
    Structure Solution CNS
    Structure Refinement CNS 1.2
     
    Software
    refinement CNS version: 1.2
    model building CNS