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X-RAY DIFFRACTION
Materials and Methods page
4L62
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.5
    Temperature 293.15
    Details 0.79M sodium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 211.99 α = 90
    b = 211.99 β = 90
    c = 282.77 γ = 120
     
    Space Group
    Space Group Name:    P 32 2 1
     
     
  •   Diffraction Hide
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 210
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type PAL/PLS BEAMLINE 5C (4A)
    Site PAL/PLS
    Beamline 5C (4A)
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.9
    Resolution(Low) 20
    Number Reflections(All) 162384
    Percent Possible(Observed) 100.0
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.9
    Resolution(Low) 19.954
    Cut-off Sigma(F) 1.34
    Number of Reflections(Observed) 162245
    Number of Reflections(R-Free) 8134
    Percent Reflections(Observed) 99.9
    R-Factor(Observed) 0.1996
    R-Work 0.1975
    R-Free 0.2383
     
    Temperature Factor Modeling
    Data Not Available
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.896
    Shell Resolution(Low) 2.9288
    Number of Reflections(R-Free) 275
    Number of Reflections(R-Work) 4986
    R-Factor(R-Work) 0.3283
    R-Factor(R-Free) 0.3943
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9288
    Shell Resolution(Low) 2.9632
    Number of Reflections(R-Free) 254
    Number of Reflections(R-Work) 5148
    R-Factor(R-Work) 0.3154
    R-Factor(R-Free) 0.3822
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9632
    Shell Resolution(Low) 2.9992
    Number of Reflections(R-Free) 287
    Number of Reflections(R-Work) 5077
    R-Factor(R-Work) 0.3057
    R-Factor(R-Free) 0.3755
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9992
    Shell Resolution(Low) 3.037
    Number of Reflections(R-Free) 252
    Number of Reflections(R-Work) 5098
    R-Factor(R-Work) 0.2989
    R-Factor(R-Free) 0.3657
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.037
    Shell Resolution(Low) 3.0769
    Number of Reflections(R-Free) 274
    Number of Reflections(R-Work) 5100
    R-Factor(R-Work) 0.276
    R-Factor(R-Free) 0.3561
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0769
    Shell Resolution(Low) 3.1189
    Number of Reflections(R-Free) 266
    Number of Reflections(R-Work) 5097
    R-Factor(R-Work) 0.2729
    R-Factor(R-Free) 0.3036
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1189
    Shell Resolution(Low) 3.1632
    Number of Reflections(R-Free) 281
    Number of Reflections(R-Work) 5092
    R-Factor(R-Work) 0.2763
    R-Factor(R-Free) 0.3313
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1632
    Shell Resolution(Low) 3.2103
    Number of Reflections(R-Free) 265
    Number of Reflections(R-Work) 5129
    R-Factor(R-Work) 0.2716
    R-Factor(R-Free) 0.314
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2103
    Shell Resolution(Low) 3.2602
    Number of Reflections(R-Free) 257
    Number of Reflections(R-Work) 5085
    R-Factor(R-Work) 0.2456
    R-Factor(R-Free) 0.2948
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2602
    Shell Resolution(Low) 3.3134
    Number of Reflections(R-Free) 287
    Number of Reflections(R-Work) 5116
    R-Factor(R-Work) 0.2272
    R-Factor(R-Free) 0.2616
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3134
    Shell Resolution(Low) 3.3703
    Number of Reflections(R-Free) 256
    Number of Reflections(R-Work) 5120
    R-Factor(R-Work) 0.2334
    R-Factor(R-Free) 0.3006
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3703
    Shell Resolution(Low) 3.4313
    Number of Reflections(R-Free) 257
    Number of Reflections(R-Work) 5133
    R-Factor(R-Work) 0.2181
    R-Factor(R-Free) 0.2632
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4313
    Shell Resolution(Low) 3.497
    Number of Reflections(R-Free) 291
    Number of Reflections(R-Work) 5060
    R-Factor(R-Work) 0.219
    R-Factor(R-Free) 0.264
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.497
    Shell Resolution(Low) 3.5679
    Number of Reflections(R-Free) 252
    Number of Reflections(R-Work) 5140
    R-Factor(R-Work) 0.2298
    R-Factor(R-Free) 0.3024
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5679
    Shell Resolution(Low) 3.6451
    Number of Reflections(R-Free) 282
    Number of Reflections(R-Work) 5125
    R-Factor(R-Work) 0.2292
    R-Factor(R-Free) 0.2696
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6451
    Shell Resolution(Low) 3.7293
    Number of Reflections(R-Free) 255
    Number of Reflections(R-Work) 5110
    R-Factor(R-Work) 0.2094
    R-Factor(R-Free) 0.2723
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7293
    Shell Resolution(Low) 3.822
    Number of Reflections(R-Free) 268
    Number of Reflections(R-Work) 5129
    R-Factor(R-Work) 0.2048
    R-Factor(R-Free) 0.256
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.822
    Shell Resolution(Low) 3.9245
    Number of Reflections(R-Free) 266
    Number of Reflections(R-Work) 5155
    R-Factor(R-Work) 0.1933
    R-Factor(R-Free) 0.2472
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9245
    Shell Resolution(Low) 4.0391
    Number of Reflections(R-Free) 252
    Number of Reflections(R-Work) 5096
    R-Factor(R-Work) 0.1823
    R-Factor(R-Free) 0.2261
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0391
    Shell Resolution(Low) 4.1683
    Number of Reflections(R-Free) 276
    Number of Reflections(R-Work) 5153
    R-Factor(R-Work) 0.1691
    R-Factor(R-Free) 0.2098
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1683
    Shell Resolution(Low) 4.3159
    Number of Reflections(R-Free) 273
    Number of Reflections(R-Work) 5129
    R-Factor(R-Work) 0.1546
    R-Factor(R-Free) 0.2017
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3159
    Shell Resolution(Low) 4.4868
    Number of Reflections(R-Free) 255
    Number of Reflections(R-Work) 5147
    R-Factor(R-Work) 0.1556
    R-Factor(R-Free) 0.2035
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4868
    Shell Resolution(Low) 4.6885
    Number of Reflections(R-Free) 275
    Number of Reflections(R-Work) 5174
    R-Factor(R-Work) 0.1568
    R-Factor(R-Free) 0.1979
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6885
    Shell Resolution(Low) 4.9321
    Number of Reflections(R-Free) 281
    Number of Reflections(R-Work) 5142
    R-Factor(R-Work) 0.1523
    R-Factor(R-Free) 0.1847
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9321
    Shell Resolution(Low) 5.2359
    Number of Reflections(R-Free) 242
    Number of Reflections(R-Work) 5198
    R-Factor(R-Work) 0.1542
    R-Factor(R-Free) 0.187
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2359
    Shell Resolution(Low) 5.6317
    Number of Reflections(R-Free) 276
    Number of Reflections(R-Work) 5170
    R-Factor(R-Work) 0.161
    R-Factor(R-Free) 0.2028
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.6317
    Shell Resolution(Low) 6.1831
    Number of Reflections(R-Free) 285
    Number of Reflections(R-Work) 5196
    R-Factor(R-Work) 0.1843
    R-Factor(R-Free) 0.2125
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.1831
    Shell Resolution(Low) 7.0432
    Number of Reflections(R-Free) 273
    Number of Reflections(R-Work) 5235
    R-Factor(R-Work) 0.1988
    R-Factor(R-Free) 0.2478
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.0432
    Shell Resolution(Low) 8.7474
    Number of Reflections(R-Free) 302
    Number of Reflections(R-Work) 5245
    R-Factor(R-Work) 0.165
    R-Factor(R-Free) 0.1755
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.7474
    Shell Resolution(Low) 19.9543
    Number of Reflections(R-Free) 319
    Number of Reflections(R-Work) 5326
    R-Factor(R-Work) 0.1657
    R-Factor(R-Free) 0.1745
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.009
    f_chiral_restr 0.094
    f_dihedral_angle_d 20.309
    f_angle_d 1.913
    f_bond_d 0.013
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 23648
    Nucleic Acid Atoms 4064
    Heterogen Atoms 0
    Solvent Atoms 209
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHENIX
    Structure Refinement PHENIX (phenix.refine: 1.8.1_1168)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.8.1_1168)
    model building PHENIX
    data collection HKL-2000