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X-RAY DIFFRACTION
Materials and Methods page
3VBA
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.9
    Temperature 293.0
    Details 25% PEG MME 2000, 0.1M Tris-HCl , pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 33.84 α = 90
    b = 107.14 β = 90
    c = 288.71 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 msc saturna200
    Collection Date 2011-04-22
     
    Diffraction Radiation
    Monochromator GRAPHITE
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SPRING-8 BEAMLINE BL26B2
    Wavelength List 1.0000
    Site SPRING-8
    Beamline BL26B2
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 2.0
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 2
    Resolution(Low) 50
    Number Reflections(Observed) 71994
    Percent Possible(Observed) 98.6
    B(Isotropic) From Wilson Plot 19.45
     
    High Resolution Shell Details
    Resolution(High) 1.98
    Resolution(Low) 2.03
    Percent Possible(All) 99.6
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.0
    Resolution(Low) 43.895
    Cut-off Sigma(F) 0.09
    Number of Reflections(Observed) 71994
    Number of Reflections(R-Free) 3571
    Percent Reflections(Observed) 98.95
    R-Factor(Observed) 0.1992
    R-Work 0.1968
    R-Free 0.2444
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 23.9456
    Anisotropic B[1][1] -0.7812
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -1.0152
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 1.7964
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0
    Shell Resolution(Low) 2.0715
    Number of Reflections(R-Free) 355
    Number of Reflections(R-Work) 6673
    R-Factor(R-Work) 0.2216
    R-Factor(R-Free) 0.2955
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0715
    Shell Resolution(Low) 2.1544
    Number of Reflections(R-Free) 338
    Number of Reflections(R-Work) 6797
    R-Factor(R-Work) 0.2056
    R-Factor(R-Free) 0.2705
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1544
    Shell Resolution(Low) 2.2525
    Number of Reflections(R-Free) 342
    Number of Reflections(R-Work) 6828
    R-Factor(R-Work) 0.1883
    R-Factor(R-Free) 0.2376
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2525
    Shell Resolution(Low) 2.3712
    Number of Reflections(R-Free) 362
    Number of Reflections(R-Work) 6694
    R-Factor(R-Work) 0.1966
    R-Factor(R-Free) 0.2701
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3712
    Shell Resolution(Low) 2.5198
    Number of Reflections(R-Free) 365
    Number of Reflections(R-Work) 6751
    R-Factor(R-Work) 0.1939
    R-Factor(R-Free) 0.2462
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5198
    Shell Resolution(Low) 2.7143
    Number of Reflections(R-Free) 356
    Number of Reflections(R-Work) 6829
    R-Factor(R-Work) 0.2063
    R-Factor(R-Free) 0.2633
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7143
    Shell Resolution(Low) 2.9874
    Number of Reflections(R-Free) 358
    Number of Reflections(R-Work) 6856
    R-Factor(R-Work) 0.207
    R-Factor(R-Free) 0.2583
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9874
    Shell Resolution(Low) 3.4195
    Number of Reflections(R-Free) 363
    Number of Reflections(R-Work) 6933
    R-Factor(R-Work) 0.1964
    R-Factor(R-Free) 0.25
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4195
    Shell Resolution(Low) 4.3077
    Number of Reflections(R-Free) 366
    Number of Reflections(R-Work) 6952
    R-Factor(R-Work) 0.1891
    R-Factor(R-Free) 0.2276
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3077
    Shell Resolution(Low) 43.9056
    Number of Reflections(R-Free) 366
    Number of Reflections(R-Work) 7110
    R-Factor(R-Work) 0.1887
    R-Factor(R-Free) 0.2075
    Percent Reflections(Observed) 97.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 15.333
    f_plane_restr 0.005
    f_chiral_restr 0.072
    f_angle_d 1.09
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 7635
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 721
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHENIX
    Structure Refinement PHENIX (phenix.refine: 1.6.4_486)
     
    Software
    data extraction pdb_extract version: 3.10
    refinement phenix