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X-RAY DIFFRACTION
Materials and Methods page
4F8R
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5.8
    Temperature 290.0
    Details 48%-54% 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 = 93.67 α = 90
    b = 109.37 β = 90
    c = 150.39 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 225 mm CCD
    Collection Date 2011-11-19
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 22-BM
    Wavelength List 1.0000
    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) 172238
    Percent Possible(Observed) 91.2
    R Merge I(Observed) 0.038
    B(Isotropic) From Wilson Plot 29.803
    Redundancy 5.7
     
    High Resolution Shell Details
    Resolution(High) 1.64
    Resolution(Low) 1.74
    Percent Possible(All) 99.9
    R Merge I(Observed) 0.476
    Mean I Over Sigma(Observed) 3.98
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 1.64
    Resolution(Low) 30.982
    Cut-off Sigma(F) 2.35
    Number of Reflections(Observed) 165495
    Number of Reflections(R-Free) 7474
    Percent Reflections(Observed) 87.69
    R-Factor(Observed) 0.1821
    R-Work 0.1811
    R-Free 0.2034
    R-Free Selection Details Inherited free reflections from 2HVI plus 5% randomly generated reflections beyond 1.98 A resolution
     
    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) 268
    Number of Reflections(R-Work) 5102
    R-Factor(R-Work) 0.2411
    R-Factor(R-Free) 0.2607
    Percent Reflections(Observed) 86.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6586
    Shell Resolution(Low) 1.6782
    Number of Reflections(R-Free) 273
    Number of Reflections(R-Work) 5187
    R-Factor(R-Work) 0.2307
    R-Factor(R-Free) 0.2662
    Percent Reflections(Observed) 88.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6782
    Shell Resolution(Low) 1.6986
    Number of Reflections(R-Free) 276
    Number of Reflections(R-Work) 5235
    R-Factor(R-Work) 0.2224
    R-Factor(R-Free) 0.2423
    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) 283
    Number of Reflections(R-Work) 5382
    R-Factor(R-Work) 0.2116
    R-Factor(R-Free) 0.2403
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7201
    Shell Resolution(Low) 1.7427
    Number of Reflections(R-Free) 282
    Number of Reflections(R-Work) 5357
    R-Factor(R-Work) 0.2047
    R-Factor(R-Free) 0.2515
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7427
    Shell Resolution(Low) 1.7666
    Number of Reflections(R-Free) 291
    Number of Reflections(R-Work) 5538
    R-Factor(R-Work) 0.2041
    R-Factor(R-Free) 0.2448
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7666
    Shell Resolution(Low) 1.7919
    Number of Reflections(R-Free) 291
    Number of Reflections(R-Work) 5529
    R-Factor(R-Work) 0.1989
    R-Factor(R-Free) 0.2463
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7919
    Shell Resolution(Low) 1.8186
    Number of Reflections(R-Free) 294
    Number of Reflections(R-Work) 5570
    R-Factor(R-Work) 0.1933
    R-Factor(R-Free) 0.2194
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8186
    Shell Resolution(Low) 1.847
    Number of Reflections(R-Free) 294
    Number of Reflections(R-Work) 5601
    R-Factor(R-Work) 0.1993
    R-Factor(R-Free) 0.2505
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.847
    Shell Resolution(Low) 1.8773
    Number of Reflections(R-Free) 293
    Number of Reflections(R-Work) 5556
    R-Factor(R-Work) 0.1929
    R-Factor(R-Free) 0.2467
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8773
    Shell Resolution(Low) 1.9097
    Number of Reflections(R-Free) 98
    Number of Reflections(R-Work) 1860
    R-Factor(R-Work) 0.1971
    R-Factor(R-Free) 0.2323
    Percent Reflections(Observed) 85.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9444
    Shell Resolution(Low) 1.9818
    Number of Reflections(R-Free) 285
    Number of Reflections(R-Work) 5396
    R-Factor(R-Work) 0.1946
    R-Factor(R-Free) 0.2384
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9818
    Shell Resolution(Low) 2.0222
    Number of Reflections(R-Free) 186
    Number of Reflections(R-Work) 5921
    R-Factor(R-Work) 0.1859
    R-Factor(R-Free) 0.2069
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0222
    Shell Resolution(Low) 2.0662
    Number of Reflections(R-Free) 210
    Number of Reflections(R-Work) 5966
    R-Factor(R-Work) 0.1834
    R-Factor(R-Free) 0.214
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0662
    Shell Resolution(Low) 2.1142
    Number of Reflections(R-Free) 235
    Number of Reflections(R-Work) 5934
    R-Factor(R-Work) 0.1761
    R-Factor(R-Free) 0.1879
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1142
    Shell Resolution(Low) 2.1671
    Number of Reflections(R-Free) 241
    Number of Reflections(R-Work) 5969
    R-Factor(R-Work) 0.1737
    R-Factor(R-Free) 0.191
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1671
    Shell Resolution(Low) 2.2257
    Number of Reflections(R-Free) 251
    Number of Reflections(R-Work) 5292
    R-Factor(R-Work) 0.1768
    R-Factor(R-Free) 0.2069
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2257
    Shell Resolution(Low) 2.2911
    Number of Reflections(R-Free) 38
    Number of Reflections(R-Work) 1190
    R-Factor(R-Work) 0.1667
    R-Factor(R-Free) 0.1844
    Percent Reflections(Observed) 86.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2911
    Shell Resolution(Low) 2.3651
    Number of Reflections(R-Free) 234
    Number of Reflections(R-Work) 5966
    R-Factor(R-Work) 0.171
    R-Factor(R-Free) 0.1985
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3651
    Shell Resolution(Low) 2.4496
    Number of Reflections(R-Free) 241
    Number of Reflections(R-Work) 6007
    R-Factor(R-Work) 0.1733
    R-Factor(R-Free) 0.1958
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4496
    Shell Resolution(Low) 2.5476
    Number of Reflections(R-Free) 249
    Number of Reflections(R-Work) 5995
    R-Factor(R-Work) 0.1741
    R-Factor(R-Free) 0.202
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5476
    Shell Resolution(Low) 2.6635
    Number of Reflections(R-Free) 255
    Number of Reflections(R-Work) 6035
    R-Factor(R-Work) 0.1786
    R-Factor(R-Free) 0.1907
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6635
    Shell Resolution(Low) 2.8038
    Number of Reflections(R-Free) 259
    Number of Reflections(R-Work) 6009
    R-Factor(R-Work) 0.1913
    R-Factor(R-Free) 0.2045
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8038
    Shell Resolution(Low) 2.9794
    Number of Reflections(R-Free) 282
    Number of Reflections(R-Work) 6010
    R-Factor(R-Work) 0.1926
    R-Factor(R-Free) 0.2282
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9794
    Shell Resolution(Low) 3.2092
    Number of Reflections(R-Free) 302
    Number of Reflections(R-Work) 6052
    R-Factor(R-Work) 0.1913
    R-Factor(R-Free) 0.2074
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2092
    Shell Resolution(Low) 3.5317
    Number of Reflections(R-Free) 312
    Number of Reflections(R-Work) 6024
    R-Factor(R-Work) 0.1693
    R-Factor(R-Free) 0.1972
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5317
    Shell Resolution(Low) 4.0418
    Number of Reflections(R-Free) 310
    Number of Reflections(R-Work) 6023
    R-Factor(R-Work) 0.1636
    R-Factor(R-Free) 0.1789
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0418
    Shell Resolution(Low) 5.0886
    Number of Reflections(R-Free) 321
    Number of Reflections(R-Work) 6127
    R-Factor(R-Work) 0.1523
    R-Factor(R-Free) 0.177
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0886
    Shell Resolution(Low) 30.987
    Number of Reflections(R-Free) 320
    Number of Reflections(R-Work) 6188
    R-Factor(R-Work) 0.2027
    R-Factor(R-Free) 0.2009
    Percent Reflections(Observed) 97.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 15.346
    f_plane_restr 0.007
    f_chiral_restr 0.076
    f_angle_d 1.384
    f_bond_d 0.011
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 9086
    Nucleic Acid Atoms 827
    Heterogen Atoms 25
    Solvent Atoms 1194
     
     
  •   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