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X-RAY DIFFRACTION
Materials and Methods page
3Q5F
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.74
    Temperature 298.0
    Details 20% PEG 4000, 0.1M sodium chloride, 0.05M magnesium chloride, 0.1M cacodylate, 2% benzamidine hydrochloride, pH 6.74, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 59.57 α = 90
    b = 59.57 β = 90
    c = 291.18 γ = 90
     
    Space Group
    Space Group Name:    P 41 21 2
     
     
  •   Diffraction Hide
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 300 mm CCD
    Collection Date 2010-03-18
     
    Diffraction Radiation
    Diffraction Protocol MAD
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 23-ID-B
    Wavelength List 1.20610, 1.25494, 1.25525
    Site APS
    Beamline 23-ID-B
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.96
    Resolution(Low) 50
    Number Reflections(Observed) 11205
    Percent Possible(Observed) 94.4
    R Merge I(Observed) 0.081
    Redundancy 12.5
     
    High Resolution Shell Details
    Resolution(High) 2.96
    Resolution(Low) 3.08
    Percent Possible(All) 63.2
    R Merge I(Observed) 0.26
    Redundancy 7.7
    Number Unique Reflections(All) 705
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MAD
    reflnsShellList 2.96
    Resolution(Low) 46.099
    Cut-off Sigma(F) 0.12
    Number of Reflections(Observed) 10606
    Number of Reflections(R-Free) 1060
    Percent Reflections(Observed) 89.44
    R-Factor(Observed) 0.2189
    R-Work 0.2135
    R-Free 0.2662
     
    Temperature Factor Modeling
    Mean Isotropic B Value 67.2251
    Anisotropic B[1][1] 13.9864
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 13.9864
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -27.9729
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.96
    Shell Resolution(Low) 3.0896
    Number of Reflections(R-Free) 75
    Number of Reflections(R-Work) 677
    R-Factor(R-Work) 0.3144
    R-Factor(R-Free) 0.491
    Percent Reflections(Observed) 53.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0896
    Shell Resolution(Low) 3.2525
    Number of Reflections(R-Free) 116
    Number of Reflections(R-Work) 1014
    R-Factor(R-Work) 0.2638
    R-Factor(R-Free) 0.3512
    Percent Reflections(Observed) 78.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2525
    Shell Resolution(Low) 3.4562
    Number of Reflections(R-Free) 128
    Number of Reflections(R-Work) 1194
    R-Factor(R-Work) 0.2159
    R-Factor(R-Free) 0.2895
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4562
    Shell Resolution(Low) 3.7229
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 1257
    R-Factor(R-Work) 0.2276
    R-Factor(R-Free) 0.2986
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7229
    Shell Resolution(Low) 4.0974
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 1268
    R-Factor(R-Work) 0.2094
    R-Factor(R-Free) 0.2688
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0974
    Shell Resolution(Low) 4.6898
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 1322
    R-Factor(R-Work) 0.185
    R-Factor(R-Free) 0.232
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6898
    Shell Resolution(Low) 5.9067
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 1340
    R-Factor(R-Work) 0.1948
    R-Factor(R-Free) 0.2571
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.9067
    Shell Resolution(Low) 46.1049
    Number of Reflections(R-Free) 160
    Number of Reflections(R-Work) 1474
    R-Factor(R-Work) 0.1971
    R-Factor(R-Free) 0.2216
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 22.281
    f_plane_restr 0.004
    f_chiral_restr 0.064
    f_angle_d 1.354
    f_bond_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2249
    Nucleic Acid Atoms 937
    Heterogen Atoms 0
    Solvent Atoms 0
     
     
  •   Software and Computing Hide
    Computing
    Data Collection JBluIce-EPICS
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL
    Structure Solution SOLVE
    Structure Refinement PHENIX (phenix.refine: 1.6.1_357)
     
    Software
    data extraction pdb_extract version: 3.10
    refinement phenix
    density modification RESOLVE version: 2.13
    phasing SOLVE
    data processing HKL