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X-RAY DIFFRACTION
Materials and Methods page
4GJD
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    Temperature 293.0
    Details reservoir: 18-21% PEG4000, 0.4-0.6 M sodium chloride, 50 mM sodium citrate, pH 4-5, protein solution: 10-15 mg/mL protein, 25 mM sodium chloride, 12.5 mM Tris, pH 8, drop: 1 uL protein solution + 1 uL reservoir, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 141.92 α = 90
    b = 141.92 β = 90
    c = 141.92 γ = 90
     
    Space Group
    Space Group Name:    P 21 3
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MAR CCD 165 mm
    Collection Date 2005-03-11
     
    Diffraction Radiation
    Monochromator double crystal Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SLS BEAMLINE X10SA
    Wavelength List 0.95577
    Site SLS
    Beamline X10SA
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Resolution(High) 2.65
    Resolution(Low) 47.3
    Number Reflections(Observed) 27679
    Percent Possible(Observed) 99.2
    R Merge I(Observed) 0.097
    B(Isotropic) From Wilson Plot 67.37
    Redundancy 4.0
     
    High Resolution Shell Details
    Resolution(High) 2.65
    Resolution(Low) 2.74
    Percent Possible(All) 99.9
    R Merge I(Observed) 0.48
    Mean I Over Sigma(Observed) 2.2
    Redundancy 3.9
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 2.65
    Resolution(Low) 44.86
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 27590
    Number of Reflections(R-Free) 2772
    Percent Reflections(Observed) 98.79
    R-Factor(Observed) 0.1844
    R-Work 0.1799
    R-Free 0.2251
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 50.07
    Anisotropic B[1][1] 0.0
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.0
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.0
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.65
    Shell Resolution(Low) 2.75
    Number of Reflections(Observed) 2792
    Number of Reflections(R-Free) 290
    Number of Reflections(R-Work) 2502
    R-Factor(R-Work) 0.2185
    R-Factor(R-Free) 0.2852
    Percent Reflections(Observed) 98.79
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    t_bond_d 0.01
    t_angle_deg 1.22
    t_omega_torsion 3.54
    t_other_torsion 17.71
     
    Coordinate Error
    Luzzati ESD(Observed) 0.289
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 5182
    Nucleic Acid Atoms 0
    Heterogen Atoms 101
    Solvent Atoms 300
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Refinement BUSTER 2.11.2
     
    Software
    refinement BUSTER version: 2.11.2
    model building MOLREP