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X-RAY DIFFRACTION
Materials and Methods page
4GVY
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 8
    Temperature 298.0
    Details Protein at 30 mg/ml, 26% PEG 6000, 0.05M HEPES, 0.1M Magnesium chloride, 0.02M Potassium ADP, 0.25M Sodium nitrate, 0.025M Sodium azide, 0.005M DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 65.39 α = 90
    b = 70.31 β = 90
    c = 80.32 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 MAR CCD 165 mm
    Collection Date 2002-09-13
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU RUH2R
    Wavelength List 1.541
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 1.0
    Observed Criterion Sigma(I) 1.0
    Resolution(High) 2.09
    Resolution(Low) 17.64
    Number Reflections(All) 20717
    Number Reflections(Observed) 20717
    Percent Possible(Observed) 92.14
     
    High Resolution Shell Details
    Resolution(High) 2.091
    Resolution(Low) 2.252
    Percent Possible(All) 81.0
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method ISOMORPHOUS WITH PDB ENTRY 1M15
    reflnsShellList 2.091
    Resolution(Low) 17.635
    Cut-off Sigma(F) 1.0
    Number of Reflections(all) 20717
    Number of Reflections(Observed) 20717
    Number of Reflections(R-Free) 636
    Percent Reflections(Observed) 92.14
    R-Factor(Observed) 0.1761
    R-Work 0.175
    R-Free 0.2109
    R-Free Selection Details Used same test set as PDB entry 1M15
     
    Temperature Factor Modeling
    Anisotropic B[1][1] -8.2654
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 15.1452
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -6.8797
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0906
    Shell Resolution(Low) 2.2517
    Number of Reflections(R-Free) 115
    Number of Reflections(R-Work) 3460
    R-Factor(R-Work) 0.2192
    R-Factor(R-Free) 0.2525
    Percent Reflections(Observed) 81.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2517
    Shell Resolution(Low) 2.4777
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 3895
    R-Factor(R-Work) 0.2007
    R-Factor(R-Free) 0.2523
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4777
    Shell Resolution(Low) 2.835
    Number of Reflections(R-Free) 123
    Number of Reflections(R-Work) 4064
    R-Factor(R-Work) 0.1992
    R-Factor(R-Free) 0.2594
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.835
    Shell Resolution(Low) 3.5669
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 4218
    R-Factor(R-Work) 0.1862
    R-Factor(R-Free) 0.2289
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5669
    Shell Resolution(Low) 17.6354
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 4444
    R-Factor(R-Work) 0.1469
    R-Factor(R-Free) 0.1642
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.006
    f_chiral_restr 0.067
    f_dihedral_angle_d 14.37
    f_angle_d 0.975
    f_bond_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2817
    Nucleic Acid Atoms 0
    Heterogen Atoms 40
    Solvent Atoms 258
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CrystalClear
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution PHENIX (phenix.refine: 1.7_650)
    Structure Refinement PHENIX (phenix.refine: 1.7_650)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7_650)
    model building PHENIX version: (phenix.refine: 1.7_650)
    data collection CrystalClear