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X-RAY DIFFRACTION
Materials and Methods page
3VFJ
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.5
    Temperature 291.0
    Details 0.2 M zinc acetate, 0.1 M sodium cacodylate 6.5, 16% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 40.32 α = 90
    b = 123.61 β = 90
    c = 156.74 γ = 90
     
    Space Group
    Space Group Name:    C 2 2 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 93
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2009-04-10
     
    Diffraction Radiation
    Monochromator Si(111)side bounce monochromator
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 24-ID-E
    Wavelength List 0.9792
    Site APS
    Beamline 24-ID-E
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.05
    Resolution(Low) 39.89
    Number Reflections(Observed) 47482
    Percent Possible(Observed) 100.0
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.05
    Resolution(Low) 39.89
    Cut-off Sigma(F) 1.39
    Number of Reflections(Observed) 47469
    Number of Reflections(R-Free) 2385
    Percent Reflections(Observed) 99.94
    R-Factor(Observed) 0.1901
    R-Work 0.188
    R-Free 0.231
     
    Temperature Factor Modeling
    Anisotropic B[1][1] 0.6758
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -4.739
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 4.0632
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.05
    Shell Resolution(Low) 2.1233
    Number of Reflections(R-Free) 254
    Number of Reflections(R-Work) 4520
    R-Factor(R-Work) 0.2567
    R-Factor(R-Free) 0.3095
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1233
    Shell Resolution(Low) 2.2083
    Number of Reflections(R-Free) 248
    Number of Reflections(R-Work) 4471
    R-Factor(R-Work) 0.2247
    R-Factor(R-Free) 0.2746
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2083
    Shell Resolution(Low) 2.3088
    Number of Reflections(R-Free) 246
    Number of Reflections(R-Work) 4476
    R-Factor(R-Work) 0.2132
    R-Factor(R-Free) 0.2542
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3088
    Shell Resolution(Low) 2.4305
    Number of Reflections(R-Free) 210
    Number of Reflections(R-Work) 4527
    R-Factor(R-Work) 0.1968
    R-Factor(R-Free) 0.2625
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4305
    Shell Resolution(Low) 2.5827
    Number of Reflections(R-Free) 221
    Number of Reflections(R-Work) 4538
    R-Factor(R-Work) 0.2021
    R-Factor(R-Free) 0.2287
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5827
    Shell Resolution(Low) 2.7821
    Number of Reflections(R-Free) 266
    Number of Reflections(R-Work) 4493
    R-Factor(R-Work) 0.1984
    R-Factor(R-Free) 0.2802
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7821
    Shell Resolution(Low) 3.062
    Number of Reflections(R-Free) 221
    Number of Reflections(R-Work) 4528
    R-Factor(R-Work) 0.1915
    R-Factor(R-Free) 0.256
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.062
    Shell Resolution(Low) 3.5048
    Number of Reflections(R-Free) 237
    Number of Reflections(R-Work) 4501
    R-Factor(R-Work) 0.1743
    R-Factor(R-Free) 0.2085
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5048
    Shell Resolution(Low) 4.4148
    Number of Reflections(R-Free) 256
    Number of Reflections(R-Work) 4512
    R-Factor(R-Work) 0.1622
    R-Factor(R-Free) 0.2055
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4148
    Shell Resolution(Low) 39.9078
    Number of Reflections(R-Free) 226
    Number of Reflections(R-Work) 4518
    R-Factor(R-Work) 0.1831
    R-Factor(R-Free) 0.2008
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.008
    f_chiral_restr 0.067
    f_dihedral_angle_d 11.954
    f_angle_d 1.045
    f_bond_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2993
    Nucleic Acid Atoms 0
    Heterogen Atoms 73
    Solvent Atoms 155
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution MOLREP
    Structure Refinement PHENIX (phenix.refine: 1.6.2_432)
     
    Software
    data extraction pdb_extract version: 3.10
    refinement phenix
    molecular replacement MOLREP
    data reduction Xscale