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X-RAY DIFFRACTION
Materials and Methods page
4HDD
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 4.6
    Temperature 298.0
    Details 100mM sodium acetate trihydrate, 0.2M ammonium sulfate, 25% PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.9
    Temperature 298.0
    Details 0.49M sodium phosphate monobasic monohydrate - 0.91M potassium phosphate dibasic, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 51.76 α = 90
    b = 51.76 β = 90
    c = 91.56 γ = 90
     
    Space Group
    Space Group Name:    I 4 2 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
    Diffrn ID 2
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type RAYONIX MX-300
    Collection Date 2011-10-06
    Detector CCD
    Type ADSC QUANTUM 315r
    Collection Date 2011-09-08
     
    Diffraction Radiation
    Monochromator Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
    Monochromator Si(111)
    Diffraction Protocol MAD
     
    Diffraction Source
    Source SYNCHROTRON
    Type CLSI BEAMLINE 08ID-1
    Wavelength List 0.9795
    Site CLSI
    Beamline 08ID-1
    Source SYNCHROTRON
    Type ALS BEAMLINE 12.3.1
    Wavelength List 0.9793, 1.116
    Site ALS
    Beamline 12.3.1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) -3.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.35
    Resolution(Low) 45.06
    Number Reflections(All) 25782
    Number Reflections(Observed) 25782
    Percent Possible(Observed) 98.6
    R Merge I(Observed) 0.032
    B(Isotropic) From Wilson Plot 21.595
     
    High Resolution Shell Details
    Resolution(High) 1.35
    Resolution(Low) 1.39
    Percent Possible(All) 98.5
    R Merge I(Observed) 0.481
    Mean I Over Sigma(Observed) 2.07
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MAD
    reflnsShellList 1.35
    Resolution(Low) 45.058
    Cut-off Sigma(F) -3.0
    Number of Reflections(all) 14001
    Number of Reflections(Observed) 14001
    Number of Reflections(R-Free) 704
    Percent Reflections(Observed) 99.41
    R-Factor(Observed) 0.1629
    R-Work 0.1618
    R-Free 0.182
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 21.7243
    Anisotropic B[1][1] -1.1799
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -1.1799
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 2.3598
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3501
    Shell Resolution(Low) 1.4543
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2600
    R-Factor(R-Work) 0.2032
    R-Factor(R-Free) 0.3067
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4543
    Shell Resolution(Low) 1.6007
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2625
    R-Factor(R-Work) 0.1529
    R-Factor(R-Free) 0.2135
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6007
    Shell Resolution(Low) 1.8323
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2662
    R-Factor(R-Work) 0.1452
    R-Factor(R-Free) 0.188
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8323
    Shell Resolution(Low) 2.3085
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2657
    R-Factor(R-Work) 0.1355
    R-Factor(R-Free) 0.1654
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3085
    Shell Resolution(Low) 45.0836
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2753
    R-Factor(R-Work) 0.1735
    R-Factor(R-Free) 0.1697
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 16.056
    f_plane_restr 0.007
    f_chiral_restr 0.091
    f_angle_d 1.437
    f_bond_d 0.014
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 522
    Nucleic Acid Atoms 0
    Heterogen Atoms 4
    Solvent Atoms 66
     
     
  •   Software and Computing Hide
    Computing
    Data Collection MxDC
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution PHENIX (1.7.3_928)
    Structure Refinement PHENIX (phenix.refine: 1.7.3_928)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction Xscale