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X-RAY DIFFRACTION
Materials and Methods page
4JKA
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion
    pH 7.5
    Temperature 298.0
    Details 15% PEG 4000, 300mM MgCl2, 100mM Tris, pH 7.5, vapor diffusion, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 76.25 α = 90
    b = 78.22 β = 90
    c = 94.37 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 300 mm CCD
    Collection Date 2010-07-02
     
    Diffraction Radiation
    Monochromator Si
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type CLSI BEAMLINE 08ID-1
    Wavelength List 0.97949
    Site CLSI
    Beamline 08ID-1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 1.0
    Observed Criterion Sigma(I) 1.0
    Resolution(High) 1.32
    Resolution(Low) 50
    Number Reflections(Observed) 126457
    Percent Possible(Observed) 95.2
    R Merge I(Observed) 0.045
    Redundancy 4.3
     
    High Resolution Shell Details
    Resolution(High) 1.32
    Resolution(Low) 1.37
    Percent Possible(All) 85.3
    R Merge I(Observed) 0.39
    Redundancy 2.3
    Number Unique Reflections(All) 11185
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.32
    Resolution(Low) 36.13
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 126324
    Number of Reflections(R-Free) 6719
    Percent Reflections(Observed) 95.13
    R-Factor(Observed) 0.1431
    R-Work 0.1419
    R-Free 0.1658
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 24.1839
    Anisotropic B[1][1] -0.17
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.18
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.0
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.32
    Shell Resolution(Low) 1.354
    Number of Reflections(R-Free) 425
    Number of Reflections(R-Work) 7491
    R-Factor(R-Work) 0.271
    R-Factor(R-Free) 0.306
    Percent Reflections(Observed) 84.59
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_sphericity_bonded 10.807
    r_sphericity_free 26.364
    r_bond_refined_d 0.01
    r_bond_other_d 0.001
    r_angle_refined_deg 1.375
    r_angle_other_deg 0.755
    r_dihedral_angle_1_deg 5.597
    r_dihedral_angle_2_deg 38.838
    r_dihedral_angle_3_deg 13.012
    r_dihedral_angle_4_deg 16.816
    r_chiral_restr 0.081
    r_gen_planes_refined 0.007
    r_gen_planes_other 0.001
    r_rigid_bond_restr 2.201
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3572
    Nucleic Acid Atoms 0
    Heterogen Atoms 10
    Solvent Atoms 661
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CLS
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution REFMAC 5.6.0117
    Structure Refinement REFMAC 5.6.0117
     
    Software
    data extraction pdb_extract version: 3.11
    refinement REFMAC5
    data reduction SCALEPACK
    data collection DENZO