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X-RAY DIFFRACTION
Materials and Methods page
4EKD
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5.5
    Temperature 277.0
    Details 12% PEG 8,000, 15 mM CoCl2, 200 mM NaCl, and 100 mM MES 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 60.25 α = 90
    b = 60.25 β = 90
    c = 345.57 γ = 90
     
    Space Group
    Space Group Name:    P 41 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 110
     
    Diffraction Detector
    Detector CCD
    Type RAYONIX MX-300
    Details KB Bimorph Mirrors
    Collection Date 2010-10-13
     
    Diffraction Radiation
    Monochromator Si(111) double crystal
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 21-ID-D
    Wavelength List 1.0782
    Site APS
    Beamline 21-ID-D
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.7
    Resolution(Low) 30
    Number Reflections(All) 12037
    Number Reflections(Observed) 11782
    Percent Possible(Observed) 64.0
    Redundancy 4.0
     
    High Resolution Shell Details
    Resolution(High) 2.7
    Resolution(Low) 2.75
    Percent Possible(All) 21.4
    Mean I Over Sigma(Observed) 1.6
    R-Sym I(Observed) 0.441
    Redundancy 2.7
    Number Unique Reflections(All) 189
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.71
    Resolution(Low) 29.98
    Number of Reflections(all) 11078
    Number of Reflections(Observed) 11078
    Number of Reflections(R-Free) 572
    Percent Reflections(Observed) 63.29
    R-Factor(All) 0.19298
    R-Factor(Observed) 0.19298
    R-Work 0.1901
    R-Free 0.2516
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 96.352
    Anisotropic B[1][1] -0.75
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.75
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 1.5
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.71
    Shell Resolution(Low) 2.782
    Number of Reflections(R-Free) 9
    Number of Reflections(R-Work) 199
    R-Factor(R-Work) 0.333
    R-Factor(R-Free) 0.37
    Percent Reflections(Observed) 16.87
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_gen_planes_other 0.001
    r_gen_planes_refined 0.004
    r_chiral_restr 0.056
    r_dihedral_angle_4_deg 14.809
    r_dihedral_angle_3_deg 17.086
    r_dihedral_angle_2_deg 39.875
    r_dihedral_angle_1_deg 5.805
    r_angle_other_deg 0.801
    r_angle_refined_deg 1.118
    r_bond_other_d 0.001
    r_bond_refined_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3696
    Nucleic Acid Atoms 0
    Heterogen Atoms 50
    Solvent Atoms 16
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHASER
    Structure Refinement REFMAC 5.6.0117
     
    Software
    refinement REFMAC version: 5.6.0117
    model building PHASER