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X-RAY DIFFRACTION
Materials and Methods page
4EZ6
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5.8
    Temperature 290.0
    Details 48%-53% Saturated Ammonium Sulfate, 2.5% MPD, 10mM MgSO4, 100mM MES (pH 5.8), VAPOR DIFFUSION, HANGING DROP, temperature 290K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 93.74 α = 90
    b = 109.51 β = 90
    c = 149.8 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 225 mm CCD
    Collection Date 2009-10-23
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 22-BM
    Wavelength List 0.97121
    Site APS
    Beamline 22-BM
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.64
    Resolution(Low) 50
    Number Reflections(Observed) 166080
    Percent Possible(Observed) 88.1
    R Merge I(Observed) 0.055
    B(Isotropic) From Wilson Plot 26.512
    Redundancy 5.1
     
    High Resolution Shell Details
    Resolution(High) 1.64
    Resolution(Low) 1.74
    Percent Possible(All) 98.3
    R Merge I(Observed) 0.457
    Mean I Over Sigma(Observed) 3.63
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 1.64
    Resolution(Low) 46.87
    Cut-off Sigma(F) 2.35
    Number of Reflections(Observed) 158215
    Number of Reflections(R-Free) 7159
    Percent Reflections(Observed) 83.97
    R-Factor(Observed) 0.1717
    R-Work 0.1708
    R-Free 0.1922
     
    Temperature Factor Modeling
    Data Not Available
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.64
    Shell Resolution(Low) 1.6586
    Number of Reflections(R-Free) 271
    Number of Reflections(R-Work) 5152
    R-Factor(R-Work) 0.2243
    R-Factor(R-Free) 0.2475
    Percent Reflections(Observed) 87.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6586
    Shell Resolution(Low) 1.6782
    Number of Reflections(R-Free) 268
    Number of Reflections(R-Work) 5095
    R-Factor(R-Work) 0.2106
    R-Factor(R-Free) 0.2639
    Percent Reflections(Observed) 87.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6782
    Shell Resolution(Low) 1.6986
    Number of Reflections(R-Free) 275
    Number of Reflections(R-Work) 5213
    R-Factor(R-Work) 0.2052
    R-Factor(R-Free) 0.2279
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6986
    Shell Resolution(Low) 1.7201
    Number of Reflections(R-Free) 276
    Number of Reflections(R-Work) 5248
    R-Factor(R-Work) 0.1924
    R-Factor(R-Free) 0.2089
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7201
    Shell Resolution(Low) 1.7428
    Number of Reflections(R-Free) 278
    Number of Reflections(R-Work) 5297
    R-Factor(R-Work) 0.1945
    R-Factor(R-Free) 0.2108
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7428
    Shell Resolution(Low) 1.7666
    Number of Reflections(R-Free) 282
    Number of Reflections(R-Work) 5354
    R-Factor(R-Work) 0.1849
    R-Factor(R-Free) 0.2185
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7666
    Shell Resolution(Low) 1.7919
    Number of Reflections(R-Free) 283
    Number of Reflections(R-Work) 5379
    R-Factor(R-Work) 0.1821
    R-Factor(R-Free) 0.2286
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7919
    Shell Resolution(Low) 1.8186
    Number of Reflections(R-Free) 286
    Number of Reflections(R-Work) 5419
    R-Factor(R-Work) 0.1768
    R-Factor(R-Free) 0.2387
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8186
    Shell Resolution(Low) 1.847
    Number of Reflections(R-Free) 284
    Number of Reflections(R-Work) 5394
    R-Factor(R-Work) 0.178
    R-Factor(R-Free) 0.2104
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.847
    Shell Resolution(Low) 1.8773
    Number of Reflections(R-Free) 282
    Number of Reflections(R-Work) 5369
    R-Factor(R-Work) 0.1757
    R-Factor(R-Free) 0.2336
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8773
    Shell Resolution(Low) 1.9097
    Number of Reflections(R-Free) 96
    Number of Reflections(R-Work) 1810
    R-Factor(R-Work) 0.1697
    R-Factor(R-Free) 0.2218
    Percent Reflections(Observed) 71.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9097
    Shell Resolution(Low) 1.9444
    Number of Reflections(R-Free) 1
    Number of Reflections(R-Work) 27
    R-Factor(R-Work) 0.2277
    R-Factor(R-Free) 0.1272
    Percent Reflections(Observed) 13.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9444
    Shell Resolution(Low) 1.9818
    Number of Reflections(R-Free) 267
    Number of Reflections(R-Work) 5048
    R-Factor(R-Work) 0.1764
    R-Factor(R-Free) 0.2057
    Percent Reflections(Observed) 85.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9818
    Shell Resolution(Low) 2.0223
    Number of Reflections(R-Free) 188
    Number of Reflections(R-Work) 5708
    R-Factor(R-Work) 0.1696
    R-Factor(R-Free) 0.2007
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0223
    Shell Resolution(Low) 2.0663
    Number of Reflections(R-Free) 202
    Number of Reflections(R-Work) 5756
    R-Factor(R-Work) 0.1604
    R-Factor(R-Free) 0.1766
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0663
    Shell Resolution(Low) 2.1143
    Number of Reflections(R-Free) 230
    Number of Reflections(R-Work) 5694
    R-Factor(R-Work) 0.1609
    R-Factor(R-Free) 0.1873
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1143
    Shell Resolution(Low) 2.1672
    Number of Reflections(R-Free) 226
    Number of Reflections(R-Work) 5796
    R-Factor(R-Work) 0.156
    R-Factor(R-Free) 0.1667
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1672
    Shell Resolution(Low) 2.2258
    Number of Reflections(R-Free) 231
    Number of Reflections(R-Work) 5044
    R-Factor(R-Work) 0.1572
    R-Factor(R-Free) 0.1848
    Percent Reflections(Observed) 88.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2258
    Shell Resolution(Low) 2.2913
    Number of Reflections(R-Free) 43
    Number of Reflections(R-Work) 1108
    R-Factor(R-Work) 0.159
    R-Factor(R-Free) 0.1592
    Percent Reflections(Observed) 73.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2913
    Shell Resolution(Low) 2.3652
    Number of Reflections(R-Free) 221
    Number of Reflections(R-Work) 5709
    R-Factor(R-Work) 0.157
    R-Factor(R-Free) 0.1932
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3652
    Shell Resolution(Low) 2.4498
    Number of Reflections(R-Free) 231
    Number of Reflections(R-Work) 5786
    R-Factor(R-Work) 0.1578
    R-Factor(R-Free) 0.1783
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4498
    Shell Resolution(Low) 2.5478
    Number of Reflections(R-Free) 247
    Number of Reflections(R-Work) 5740
    R-Factor(R-Work) 0.1596
    R-Factor(R-Free) 0.1767
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5478
    Shell Resolution(Low) 2.6638
    Number of Reflections(R-Free) 242
    Number of Reflections(R-Work) 5765
    R-Factor(R-Work) 0.1655
    R-Factor(R-Free) 0.1857
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6638
    Shell Resolution(Low) 2.8042
    Number of Reflections(R-Free) 247
    Number of Reflections(R-Work) 5705
    R-Factor(R-Work) 0.1726
    R-Factor(R-Free) 0.1782
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8042
    Shell Resolution(Low) 2.9799
    Number of Reflections(R-Free) 264
    Number of Reflections(R-Work) 5695
    R-Factor(R-Work) 0.1769
    R-Factor(R-Free) 0.1894
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9799
    Shell Resolution(Low) 3.2099
    Number of Reflections(R-Free) 283
    Number of Reflections(R-Work) 5704
    R-Factor(R-Work) 0.1759
    R-Factor(R-Free) 0.2052
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2099
    Shell Resolution(Low) 3.5328
    Number of Reflections(R-Free) 297
    Number of Reflections(R-Work) 5602
    R-Factor(R-Work) 0.1629
    R-Factor(R-Free) 0.1724
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5328
    Shell Resolution(Low) 4.0438
    Number of Reflections(R-Free) 280
    Number of Reflections(R-Work) 5393
    R-Factor(R-Work) 0.1734
    R-Factor(R-Free) 0.1912
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0438
    Shell Resolution(Low) 5.0938
    Number of Reflections(R-Free) 287
    Number of Reflections(R-Work) 5580
    R-Factor(R-Work) 0.1453
    R-Factor(R-Free) 0.155
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0938
    Shell Resolution(Low) 46.8891
    Number of Reflections(R-Free) 291
    Number of Reflections(R-Work) 5466
    R-Factor(R-Work) 0.1996
    R-Factor(R-Free) 0.2133
    Percent Reflections(Observed) 86.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.007
    f_chiral_restr 0.076
    f_dihedral_angle_d 15.579
    f_angle_d 1.355
    f_bond_d 0.01
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 9046
    Nucleic Acid Atoms 832
    Heterogen Atoms 73
    Solvent Atoms 1364
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Refinement PHENIX (phenix.refine: dev_1026)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction Xscale