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X-RAY DIFFRACTION
Materials and Methods page
4A74
  •   Crystallization Hide
    Crystallization Experiments
    pH 5.8
    Details 60 MM NA2HPO4 PH 6.0; 15% PEG 1000.
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 40.46 α = 90
    b = 87.42 β = 91.46
    c = 62.23 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD (MX-225)
    Type MARRESEARCH
    Collection Date 2009-06-15
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SLS BEAMLINE X06DA
    Wavelength 0.9793
    Site SLS
    Beamline X06DA
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 3.0
    Resolution(High) 1.47
    Resolution(Low) 43.71
    Number Reflections(Observed) 69371
    Percent Possible(Observed) 95.4
    R Merge I(Observed) 0.08
    B(Isotropic) From Wilson Plot 11.12
    Redundancy 3.6
     
    High Resolution Shell Details
    Resolution(High) 1.47
    Resolution(Low) 1.55
    Percent Possible(All) 95.0
    R Merge I(Observed) 0.6
    Mean I Over Sigma(Observed) 2.4
    Redundancy 3.6
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.476
    Resolution(Low) 40.443
    Cut-off Sigma(F) 1.99
    Number of Reflections(Observed) 72247
    Number of Reflections(R-Free) 6357
    Percent Reflections(Observed) 88.35
    R-Factor(Observed) 0.2181
    R-Work 0.2161
    R-Free 0.2565
     
    Temperature Factor Modeling
    Mean Isotropic B Value 15.113
    Anisotropic B[1][1] 0.6181
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -0.6279
    Anisotropic B[2][2] -2.8285
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 2.2104
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4758
    Shell Resolution(Low) 1.4926
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2926
    R-Factor(R-Work) 0.3082
    R-Factor(R-Free) 0.3082
    Percent Reflections(Observed) 64.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4926
    Shell Resolution(Low) 1.5101
    Number of Reflections(R-Free) 223
    Number of Reflections(R-Work) 4332
    R-Factor(R-Work) 0.2512
    R-Factor(R-Free) 0.2898
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5101
    Shell Resolution(Low) 1.5285
    Number of Reflections(R-Free) 253
    Number of Reflections(R-Work) 4338
    R-Factor(R-Work) 0.2387
    R-Factor(R-Free) 0.2698
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5285
    Shell Resolution(Low) 1.5479
    Number of Reflections(R-Free) 231
    Number of Reflections(R-Work) 4399
    R-Factor(R-Work) 0.2334
    R-Factor(R-Free) 0.2521
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5479
    Shell Resolution(Low) 1.5683
    Number of Reflections(R-Free) 233
    Number of Reflections(R-Work) 4371
    R-Factor(R-Work) 0.2258
    R-Factor(R-Free) 0.242
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5683
    Shell Resolution(Low) 1.5898
    Number of Reflections(R-Free) 214
    Number of Reflections(R-Work) 4385
    R-Factor(R-Work) 0.2241
    R-Factor(R-Free) 0.262
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5898
    Shell Resolution(Low) 1.6125
    Number of Reflections(R-Free) 237
    Number of Reflections(R-Work) 4406
    R-Factor(R-Work) 0.2197
    R-Factor(R-Free) 0.2796
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6125
    Shell Resolution(Low) 1.6365
    Number of Reflections(R-Free) 239
    Number of Reflections(R-Work) 4389
    R-Factor(R-Work) 0.2141
    R-Factor(R-Free) 0.2736
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6365
    Shell Resolution(Low) 1.6621
    Number of Reflections(R-Free) 211
    Number of Reflections(R-Work) 4399
    R-Factor(R-Work) 0.2035
    R-Factor(R-Free) 0.2281
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6621
    Shell Resolution(Low) 1.6894
    Number of Reflections(R-Free) 277
    Number of Reflections(R-Work) 4464
    R-Factor(R-Work) 0.1988
    R-Factor(R-Free) 0.2512
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6894
    Shell Resolution(Low) 1.7185
    Number of Reflections(R-Free) 220
    Number of Reflections(R-Work) 4393
    R-Factor(R-Work) 0.1982
    R-Factor(R-Free) 0.2375
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7185
    Shell Resolution(Low) 1.7497
    Number of Reflections(R-Free) 239
    Number of Reflections(R-Work) 4475
    R-Factor(R-Work) 0.1983
    R-Factor(R-Free) 0.2504
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7497
    Shell Resolution(Low) 1.7834
    Number of Reflections(R-Free) 176
    Number of Reflections(R-Work) 4500
    R-Factor(R-Work) 0.1967
    R-Factor(R-Free) 0.252
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7834
    Shell Resolution(Low) 1.8198
    Number of Reflections(R-Free) 203
    Number of Reflections(R-Work) 4465
    R-Factor(R-Work) 0.1924
    R-Factor(R-Free) 0.2473
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8198
    Shell Resolution(Low) 1.8594
    Number of Reflections(R-Free) 254
    Number of Reflections(R-Work) 4400
    R-Factor(R-Work) 0.1858
    R-Factor(R-Free) 0.228
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8594
    Shell Resolution(Low) 1.9026
    Number of Reflections(R-Free) 181
    Number of Reflections(R-Work) 2863
    R-Factor(R-Work) 0.2201
    R-Factor(R-Free) 0.2792
    Percent Reflections(Observed) 64.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9026
    Shell Resolution(Low) 1.9502
    Number of Reflections(R-Free) 59
    Number of Reflections(R-Work) 1178
    R-Factor(R-Work) 0.385
    R-Factor(R-Free) 0.5799
    Percent Reflections(Observed) 27.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9502
    Shell Resolution(Low) 2.0029
    Number of Reflections(R-Free) 203
    Number of Reflections(R-Work) 3440
    R-Factor(R-Work) 0.2405
    R-Factor(R-Free) 0.2532
    Percent Reflections(Observed) 76.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0029
    Shell Resolution(Low) 2.0619
    Number of Reflections(R-Free) 244
    Number of Reflections(R-Work) 4479
    R-Factor(R-Work) 0.1903
    R-Factor(R-Free) 0.2473
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0619
    Shell Resolution(Low) 2.1284
    Number of Reflections(R-Free) 244
    Number of Reflections(R-Work) 4496
    R-Factor(R-Work) 0.1877
    R-Factor(R-Free) 0.2154
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1284
    Shell Resolution(Low) 2.2045
    Number of Reflections(R-Free) 220
    Number of Reflections(R-Work) 4249
    R-Factor(R-Work) 0.1933
    R-Factor(R-Free) 0.264
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2045
    Shell Resolution(Low) 2.2927
    Number of Reflections(R-Free) 58
    Number of Reflections(R-Work) 1242
    R-Factor(R-Work) 0.4758
    R-Factor(R-Free) 0.621
    Percent Reflections(Observed) 27.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2927
    Shell Resolution(Low) 2.3971
    Number of Reflections(R-Free) 248
    Number of Reflections(R-Work) 3911
    R-Factor(R-Work) 0.2086
    R-Factor(R-Free) 0.2404
    Percent Reflections(Observed) 87.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3971
    Shell Resolution(Low) 2.5234
    Number of Reflections(R-Free) 225
    Number of Reflections(R-Work) 4452
    R-Factor(R-Work) 0.1992
    R-Factor(R-Free) 0.2776
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5234
    Shell Resolution(Low) 2.6815
    Number of Reflections(R-Free) 198
    Number of Reflections(R-Work) 4504
    R-Factor(R-Work) 0.2087
    R-Factor(R-Free) 0.228
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6815
    Shell Resolution(Low) 2.8885
    Number of Reflections(R-Free) 246
    Number of Reflections(R-Work) 4412
    R-Factor(R-Work) 0.2157
    R-Factor(R-Free) 0.2692
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8885
    Shell Resolution(Low) 3.1791
    Number of Reflections(R-Free) 249
    Number of Reflections(R-Work) 4378
    R-Factor(R-Work) 0.2026
    R-Factor(R-Free) 0.2725
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1791
    Shell Resolution(Low) 3.6388
    Number of Reflections(R-Free) 202
    Number of Reflections(R-Work) 3993
    R-Factor(R-Work) 0.1836
    R-Factor(R-Free) 0.2281
    Percent Reflections(Observed) 87.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6388
    Shell Resolution(Low) 4.5835
    Number of Reflections(R-Free) 204
    Number of Reflections(R-Work) 3668
    R-Factor(R-Work) 0.1787
    R-Factor(R-Free) 0.1891
    Percent Reflections(Observed) 81.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5835
    Shell Resolution(Low) 40.4581
    Number of Reflections(R-Free) 219
    Number of Reflections(R-Work) 4408
    R-Factor(R-Work) 0.1896
    R-Factor(R-Free) 0.2197
    Percent Reflections(Observed) 97.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.004
    f_chiral_restr 0.08
    f_dihedral_angle_d 16.998
    f_angle_d 1.254
    f_bond_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3425
    Nucleic Acid Atoms 0
    Heterogen Atoms 64
    Solvent Atoms 813
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution AMORE
    Structure Refinement PHENIX (PHENIX.REFINE)
     
    Software
    refinement PHENIX version: (PHENIX.REFINE)
    model building AMORE