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X-RAY DIFFRACTION
Materials and Methods page
3PKZ
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7
    Temperature 292.0
    Details 1.8M Ammonium Sulfate, 100 mM HEPES pH 7.0, 20% Ethylene Glycol, 5% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 292K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 128.21 α = 90
    b = 128.21 β = 90
    c = 182.01 γ = 120
     
    Space Group
    Space Group Name:    P 65
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 73
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 225 mm CCD
    Collection Date 2009-12-19
    Detector CCD
    Type ADSC QUANTUM 315r
    Collection Date 2009-11-23
     
    Diffraction Radiation
    Monochromator Si220
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 21-ID-F
    Wavelength List 0.9787
    Site APS
    Beamline 21-ID-F
    Source SYNCHROTRON
    Type APS BEAMLINE 19-ID
    Wavelength List 0.9794
    Site APS
    Beamline 19-ID
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 5.9
    Observed Criterion Sigma(I) 170.6
    Resolution(High) 1.8
    Resolution(Low) 100
    Number Reflections(All) 156340
    Number Reflections(Observed) 140384
    Percent Possible(Observed) 90.0
     
    High Resolution Shell Details
    Resolution(High) 1.83
    Resolution(Low) 1.86
    R Merge I(Observed) 0.966
    Mean I Over Sigma(Observed) 1.79
    R-Sym I(Observed) 0.825
    Redundancy 6.3
    Number Unique Reflections(All) 7798
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method SAD
    reflnsShellList 1.8
    Resolution(Low) 41.97
    Number of Reflections(all) 156340
    Number of Reflections(Observed) 140384
    Number of Reflections(R-Free) 7398
    Percent Reflections(Observed) 94.48
    R-Factor(Observed) 0.20886
    R-Work 0.2069
    R-Free 0.24645
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 32.085
    Anisotropic B[1][1] 0.17
    Anisotropic B[1][2] 0.09
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.17
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.26
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.799
    Shell Resolution(Low) 1.846
    Number of Reflections(R-Free) 451
    Number of Reflections(R-Work) 8745
    R-Factor(R-Work) 0.289
    R-Factor(R-Free) 0.349
    Percent Reflections(Observed) 79.62
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 2.025
    r_scbond_it 1.207
    r_mcangle_it 0.735
    r_mcbond_it 0.373
    r_gen_planes_refined 0.003
    r_chiral_restr 0.065
    r_dihedral_angle_4_deg 17.489
    r_dihedral_angle_3_deg 13.668
    r_dihedral_angle_2_deg 37.767
    r_dihedral_angle_1_deg 4.56
    r_angle_refined_deg 0.936
    r_bond_refined_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 12032
    Nucleic Acid Atoms 0
    Heterogen Atoms 120
    Solvent Atoms 890
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-3000
    Data Reduction (intensity integration) HKL-3000
    Data Reduction (data scaling) HKL-3000
    Structure Solution SOLVE
    Structure Refinement REFMAC 5.5.0072
     
    Software
    refinement REFMAC version: 5.5.0072
    model building SOLVE
    data collection HKL-3000