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X-RAY DIFFRACTION
Materials and Methods page
4EB2
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 3.4
    Temperature 293.0
    Details 0.01 M sodium acetate, 25% saturated ammonium sulfate, 0.1 M glycin/HCl buffer, pH 3.4, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 107.06 α = 90
    b = 107.06 β = 90
    c = 311.2 γ = 120
     
    Space Group
    Space Group Name:    P 65 2 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MAR CCD 165 mm
    Collection Date 2011-10-23
     
    Diffraction Radiation
    Monochromator horizontally focusing Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type EMBL/DESY, HAMBURG BEAMLINE X13
    Wavelength List 0.81
    Site EMBL/DESY, HAMBURG
    Beamline X13
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.94
    Resolution(Low) 29.5
    Number Reflections(All) 78881
    Number Reflections(Observed) 77457
    Percent Possible(Observed) 98.2
    R Merge I(Observed) 0.172
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.94
    Resolution(Low) 7.998
    Cut-off Sigma(F) 1.99
    Number of Reflections(all) 77457
    Number of Reflections(Observed) 76180
    Number of Reflections(R-Free) 3809
    Percent Reflections(Observed) 98.25
    R-Factor(Observed) 0.1827
    R-Work 0.1803
    R-Free 0.2256
     
    Temperature Factor Modeling
    Anisotropic B[1][1] 1.019
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 1.019
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -2.0381
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.94
    Shell Resolution(Low) 1.9642
    Number of Reflections(R-Free) 126
    Number of Reflections(R-Work) 2395
    R-Factor(R-Work) 0.438
    R-Factor(R-Free) 0.478
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9642
    Shell Resolution(Low) 1.9897
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2673
    R-Factor(R-Work) 0.3422
    R-Factor(R-Free) 0.3657
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9897
    Shell Resolution(Low) 2.0165
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2641
    R-Factor(R-Work) 0.3112
    R-Factor(R-Free) 0.3608
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0165
    Shell Resolution(Low) 2.0448
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2585
    R-Factor(R-Work) 0.2996
    R-Factor(R-Free) 0.3691
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0448
    Shell Resolution(Low) 2.0748
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2624
    R-Factor(R-Work) 0.2796
    R-Factor(R-Free) 0.3235
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0748
    Shell Resolution(Low) 2.1067
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2613
    R-Factor(R-Work) 0.2522
    R-Factor(R-Free) 0.2736
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1067
    Shell Resolution(Low) 2.1406
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2624
    R-Factor(R-Work) 0.2372
    R-Factor(R-Free) 0.2985
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1406
    Shell Resolution(Low) 2.1768
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2607
    R-Factor(R-Work) 0.2527
    R-Factor(R-Free) 0.3219
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1768
    Shell Resolution(Low) 2.2155
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2598
    R-Factor(R-Work) 0.2705
    R-Factor(R-Free) 0.3492
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2155
    Shell Resolution(Low) 2.2572
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2606
    R-Factor(R-Work) 0.2701
    R-Factor(R-Free) 0.3935
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2572
    Shell Resolution(Low) 2.3022
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2647
    R-Factor(R-Work) 0.2602
    R-Factor(R-Free) 0.3117
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3022
    Shell Resolution(Low) 2.351
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2680
    R-Factor(R-Work) 0.2241
    R-Factor(R-Free) 0.3194
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.351
    Shell Resolution(Low) 2.4043
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2658
    R-Factor(R-Work) 0.1961
    R-Factor(R-Free) 0.2621
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4043
    Shell Resolution(Low) 2.4627
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2667
    R-Factor(R-Work) 0.1713
    R-Factor(R-Free) 0.2543
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4627
    Shell Resolution(Low) 2.5272
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2667
    R-Factor(R-Work) 0.1783
    R-Factor(R-Free) 0.2314
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5272
    Shell Resolution(Low) 2.5991
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2662
    R-Factor(R-Work) 0.1796
    R-Factor(R-Free) 0.2253
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5991
    Shell Resolution(Low) 2.6799
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2695
    R-Factor(R-Work) 0.1963
    R-Factor(R-Free) 0.2827
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6799
    Shell Resolution(Low) 2.7719
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2689
    R-Factor(R-Work) 0.1898
    R-Factor(R-Free) 0.2126
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7719
    Shell Resolution(Low) 2.8779
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2729
    R-Factor(R-Work) 0.1671
    R-Factor(R-Free) 0.249
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8779
    Shell Resolution(Low) 3.0022
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2741
    R-Factor(R-Work) 0.1608
    R-Factor(R-Free) 0.2055
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0022
    Shell Resolution(Low) 3.1513
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2754
    R-Factor(R-Work) 0.1586
    R-Factor(R-Free) 0.2372
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1513
    Shell Resolution(Low) 3.3352
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2739
    R-Factor(R-Work) 0.1762
    R-Factor(R-Free) 0.2107
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3352
    Shell Resolution(Low) 3.5713
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2780
    R-Factor(R-Work) 0.1632
    R-Factor(R-Free) 0.2183
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5713
    Shell Resolution(Low) 3.8926
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2756
    R-Factor(R-Work) 0.147
    R-Factor(R-Free) 0.1876
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8926
    Shell Resolution(Low) 4.3734
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2788
    R-Factor(R-Work) 0.122
    R-Factor(R-Free) 0.1532
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3734
    Shell Resolution(Low) 5.2389
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2832
    R-Factor(R-Work) 0.1303
    R-Factor(R-Free) 0.1476
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2389
    Shell Resolution(Low) 7.9976
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2921
    R-Factor(R-Work) 0.1946
    R-Factor(R-Free) 0.2306
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.004
    f_chiral_restr 0.071
    f_dihedral_angle_d 13.344
    f_angle_d 1.011
    f_bond_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3916
    Nucleic Acid Atoms 0
    Heterogen Atoms 177
    Solvent Atoms 231
     
     
  •   Software and Computing Hide
    Computing
    Data Collection DNA
    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: 3.10
    refinement phenix
    molecular replacement Phaser
    data reduction Xscale
    data collection DENZO