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X-RAY DIFFRACTION
Materials and Methods page
4IM7
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion, sitting drop
    pH 7.5
    Temperature 282.0
    Details Protein solution was at 10 mg/mL containing 20 mM Tris (pH 7.5) and 100 mM NaCl. Mother liqueur contained 1.7 M ammonium sulfate, 0.085 M Hepes (pH 7.5), 1.7% PEG 400 and 15% glycerol, vapor diffusion, sitting drop, temperature 282K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 92.49 α = 90
    b = 92.49 β = 90
    c = 136 γ = 120
     
    Space Group
    Space Group Name:    P 31 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type RAYONIX MX-225
    Collection Date 2012-04-02
     
    Diffraction Radiation
    Monochromator C(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 21-ID-F
    Wavelength List 0.97872
    Site APS
    Beamline 21-ID-F
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.9
    Resolution(Low) 30
    Number Reflections(Observed) 53597
    Percent Possible(Observed) 99.9
    B(Isotropic) From Wilson Plot 27.297
     
    High Resolution Shell Details
    Resolution(High) 1.9
    Resolution(Low) 1.95
    Percent Possible(All) 99.9
    R Merge I(Observed) 0.611
    Mean I Over Sigma(Observed) 2.55
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.9
    Resolution(Low) 29.551
    Cut-off Sigma(F) 2.02
    Number of Reflections(all) 53647
    Number of Reflections(Observed) 53593
    Number of Reflections(R-Free) 2679
    Percent Reflections(Observed) 99.94
    R-Factor(Observed) 0.1496
    R-Work 0.1484
    R-Free 0.1728
    R-Free Selection Details random
     
    Temperature Factor Modeling
    Mean Isotropic B Value 23.6144
    Anisotropic B[1][1] -0.0825
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.0825
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.165
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9001
    Shell Resolution(Low) 1.9346
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2666
    R-Factor(R-Work) 0.2092
    R-Factor(R-Free) 0.2514
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9346
    Shell Resolution(Low) 1.9718
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2639
    R-Factor(R-Work) 0.1986
    R-Factor(R-Free) 0.244
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9718
    Shell Resolution(Low) 2.0121
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2645
    R-Factor(R-Work) 0.1871
    R-Factor(R-Free) 0.2495
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0121
    Shell Resolution(Low) 2.0558
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2660
    R-Factor(R-Work) 0.1676
    R-Factor(R-Free) 0.2108
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0558
    Shell Resolution(Low) 2.1036
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2636
    R-Factor(R-Work) 0.1593
    R-Factor(R-Free) 0.1867
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1036
    Shell Resolution(Low) 2.1562
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2634
    R-Factor(R-Work) 0.1459
    R-Factor(R-Free) 0.1979
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1562
    Shell Resolution(Low) 2.2145
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2648
    R-Factor(R-Work) 0.144
    R-Factor(R-Free) 0.1731
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2145
    Shell Resolution(Low) 2.2796
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2642
    R-Factor(R-Work) 0.1404
    R-Factor(R-Free) 0.193
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2796
    Shell Resolution(Low) 2.3532
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2688
    R-Factor(R-Work) 0.1387
    R-Factor(R-Free) 0.1843
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3532
    Shell Resolution(Low) 2.4373
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2648
    R-Factor(R-Work) 0.1416
    R-Factor(R-Free) 0.179
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4373
    Shell Resolution(Low) 2.5348
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2671
    R-Factor(R-Work) 0.1421
    R-Factor(R-Free) 0.1757
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5348
    Shell Resolution(Low) 2.6501
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2665
    R-Factor(R-Work) 0.146
    R-Factor(R-Free) 0.1644
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6501
    Shell Resolution(Low) 2.7897
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2675
    R-Factor(R-Work) 0.1486
    R-Factor(R-Free) 0.178
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7897
    Shell Resolution(Low) 2.9643
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2673
    R-Factor(R-Work) 0.1622
    R-Factor(R-Free) 0.1912
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9643
    Shell Resolution(Low) 3.193
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2705
    R-Factor(R-Work) 0.1557
    R-Factor(R-Free) 0.1653
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.193
    Shell Resolution(Low) 3.5138
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2690
    R-Factor(R-Work) 0.1481
    R-Factor(R-Free) 0.1539
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5138
    Shell Resolution(Low) 4.0212
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2727
    R-Factor(R-Work) 0.1309
    R-Factor(R-Free) 0.1494
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0212
    Shell Resolution(Low) 5.0622
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2735
    R-Factor(R-Work) 0.119
    R-Factor(R-Free) 0.1323
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0622
    Shell Resolution(Low) 29.5547
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2867
    R-Factor(R-Work) 0.1579
    R-Factor(R-Free) 0.1601
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 15.0
    f_plane_restr 0.004
    f_chiral_restr 0.072
    f_angle_d 1.105
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3758
    Nucleic Acid Atoms 0
    Heterogen Atoms 62
    Solvent Atoms 471
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.7.3_928)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    molecular replacement Phaser
    data reduction Xscale