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X-RAY DIFFRACTION
Materials and Methods page
4IJB
  •   Crystallization Hide
    Crystallization Experiments
    Method Microbatch crystallization under oil
    pH 6.5
    Temperature 277.0
    Details 30% PEG 8000, 0.2M sodium acetate, 0.1M sodium cacodylate, pH 6.5, Microbatch crystallization under oil, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 35.32 α = 90
    b = 60.19 β = 90
    c = 110.56 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 ADSC QUANTUM 315
    Collection Date 2012-12-06
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 24-ID-E
    Wavelength List 0.97921
    Site APS
    Beamline 24-ID-E
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.74
    Resolution(Low) 40.58
    Number Reflections(All) 46740
    Number Reflections(Observed) 46740
    Percent Possible(Observed) 100.0
    R Merge I(Observed) 0.089
    B(Isotropic) From Wilson Plot 19.9
    Redundancy 10.6
     
    High Resolution Shell Details
    Resolution(High) 1.739
    Resolution(Low) 1.85
    Percent Possible(All) 99.9
    R Merge I(Observed) 0.949
    Mean I Over Sigma(Observed) 2.3
    Redundancy 10.8
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method SAD
    reflnsShellList 1.739
    Resolution(Low) 25.499
    Cut-off Sigma(F) 1.21
    Number of Reflections(Observed) 46732
    Number of Reflections(R-Free) 2401
    Percent Reflections(Observed) 99.97
    R-Factor(Observed) 0.1851
    R-Work 0.1843
    R-Free 0.1998
     
    Temperature Factor Modeling
    Anisotropic B[1][1] -3.419
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 4.8031
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -1.3841
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7395
    Shell Resolution(Low) 1.775
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2618
    R-Factor(R-Work) 0.3574
    R-Factor(R-Free) 0.3743
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.775
    Shell Resolution(Low) 1.8136
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2570
    R-Factor(R-Work) 0.3159
    R-Factor(R-Free) 0.3085
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8136
    Shell Resolution(Low) 1.8557
    Number of Reflections(R-Free) 116
    Number of Reflections(R-Work) 2671
    R-Factor(R-Work) 0.2712
    R-Factor(R-Free) 0.2609
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8557
    Shell Resolution(Low) 1.9021
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2564
    R-Factor(R-Work) 0.2369
    R-Factor(R-Free) 0.2694
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9021
    Shell Resolution(Low) 1.9535
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2644
    R-Factor(R-Work) 0.1976
    R-Factor(R-Free) 0.2163
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9535
    Shell Resolution(Low) 2.011
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2583
    R-Factor(R-Work) 0.1907
    R-Factor(R-Free) 0.1792
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.011
    Shell Resolution(Low) 2.0759
    Number of Reflections(R-Free) 160
    Number of Reflections(R-Work) 2617
    R-Factor(R-Work) 0.1844
    R-Factor(R-Free) 0.203
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0759
    Shell Resolution(Low) 2.15
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2567
    R-Factor(R-Work) 0.1911
    R-Factor(R-Free) 0.2169
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.15
    Shell Resolution(Low) 2.2361
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2607
    R-Factor(R-Work) 0.1715
    R-Factor(R-Free) 0.19
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2361
    Shell Resolution(Low) 2.3378
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2621
    R-Factor(R-Work) 0.1725
    R-Factor(R-Free) 0.18
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3378
    Shell Resolution(Low) 2.4609
    Number of Reflections(R-Free) 161
    Number of Reflections(R-Work) 2560
    R-Factor(R-Work) 0.177
    R-Factor(R-Free) 0.1957
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4609
    Shell Resolution(Low) 2.615
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2627
    R-Factor(R-Work) 0.1759
    R-Factor(R-Free) 0.2008
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.615
    Shell Resolution(Low) 2.8166
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2606
    R-Factor(R-Work) 0.1768
    R-Factor(R-Free) 0.1889
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8166
    Shell Resolution(Low) 3.0997
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2603
    R-Factor(R-Work) 0.1746
    R-Factor(R-Free) 0.214
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0997
    Shell Resolution(Low) 3.5472
    Number of Reflections(R-Free) 112
    Number of Reflections(R-Work) 2650
    R-Factor(R-Work) 0.1669
    R-Factor(R-Free) 0.1928
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5472
    Shell Resolution(Low) 4.4651
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2609
    R-Factor(R-Work) 0.1522
    R-Factor(R-Free) 0.1636
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4651
    Shell Resolution(Low) 25.5022
    Number of Reflections(R-Free) 122
    Number of Reflections(R-Work) 2614
    R-Factor(R-Work) 0.184
    R-Factor(R-Free) 0.1861
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.006
    f_chiral_restr 0.101
    f_dihedral_angle_d 13.723
    f_angle_d 1.471
    f_bond_d 0.009
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1964
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 178
     
     
  •   Software and Computing Hide
    Computing
    Data Collection NE-CAT Remote Access
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XScale
    Structure Solution phenix.autosol
    Structure Refinement PHENIX (phenix.refine: 1.7.2_869)
     
    Software
    data extraction pdb_extract version: 3.100
    refinement phenix