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X-RAY DIFFRACTION
Materials and Methods page
4HCB
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 6
    Temperature 293.0
    Details 1.65-1.68 M ammonium sulfate, 6.5-6.8% v/v 2-propanol, 0.1 M sodium citrate tribasic dihydrate pH 6.0 and 5 mM phenol, VAPOR DIFFUSION, SITTING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 62.54 α = 90
    b = 107.29 β = 90
    c = 157.57 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315r
    Collection Date 2011-06-22
     
    Diffraction Radiation
    Monochromator GRAPHITE
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRF BEAMLINE BL17U
    Wavelength List 1.0720
    Site SSRF
    Beamline BL17U
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2
    Resolution(Low) 50
    Number Reflections(All) 72101
    Number Reflections(Observed) 71457
    Percent Possible(Observed) 99.1
    R Merge I(Observed) 0.083
    Redundancy 8.3
     
    High Resolution Shell Details
    Resolution(High) 2.0
    Resolution(Low) 2.07
    Percent Possible(All) 99.7
    R Merge I(Observed) 0.297
    Redundancy 8.3
    Number Unique Reflections(All) 7094
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.0
    Resolution(Low) 37.663
    Cut-off Sigma(F) 1.34
    Number of Reflections(all) 72101
    Number of Reflections(Observed) 71392
    Number of Reflections(R-Free) 3605
    Percent Reflections(Observed) 98.59
    R-Factor(Observed) 0.1849
    R-Work 0.1828
    R-Free 0.2244
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 32.88
    Anisotropic B[1][1] 2.1914
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 2.3433
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -4.5347
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0
    Shell Resolution(Low) 2.0266
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 2213
    R-Factor(R-Work) 0.1976
    R-Factor(R-Free) 0.2823
    Percent Reflections(Observed) 85.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0266
    Shell Resolution(Low) 2.0544
    Number of Reflections(R-Free) 124
    Number of Reflections(R-Work) 2607
    R-Factor(R-Work) 0.1998
    R-Factor(R-Free) 0.2454
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0544
    Shell Resolution(Low) 2.0837
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2612
    R-Factor(R-Work) 0.1941
    R-Factor(R-Free) 0.2612
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0837
    Shell Resolution(Low) 2.1148
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2606
    R-Factor(R-Work) 0.1882
    R-Factor(R-Free) 0.2831
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1148
    Shell Resolution(Low) 2.1479
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2601
    R-Factor(R-Work) 0.1931
    R-Factor(R-Free) 0.2383
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1479
    Shell Resolution(Low) 2.1831
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2593
    R-Factor(R-Work) 0.1853
    R-Factor(R-Free) 0.2642
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1831
    Shell Resolution(Low) 2.2207
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2615
    R-Factor(R-Work) 0.1909
    R-Factor(R-Free) 0.2489
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2207
    Shell Resolution(Low) 2.2611
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 2611
    R-Factor(R-Work) 0.1832
    R-Factor(R-Free) 0.2311
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2611
    Shell Resolution(Low) 2.3046
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2587
    R-Factor(R-Work) 0.1818
    R-Factor(R-Free) 0.2402
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3046
    Shell Resolution(Low) 2.3516
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2616
    R-Factor(R-Work) 0.1868
    R-Factor(R-Free) 0.2449
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3516
    Shell Resolution(Low) 2.4027
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2634
    R-Factor(R-Work) 0.1859
    R-Factor(R-Free) 0.2352
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4027
    Shell Resolution(Low) 2.4586
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2588
    R-Factor(R-Work) 0.1911
    R-Factor(R-Free) 0.2691
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4586
    Shell Resolution(Low) 2.5201
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2618
    R-Factor(R-Work) 0.1947
    R-Factor(R-Free) 0.2555
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5201
    Shell Resolution(Low) 2.5882
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2628
    R-Factor(R-Work) 0.2064
    R-Factor(R-Free) 0.2963
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5882
    Shell Resolution(Low) 2.6644
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2616
    R-Factor(R-Work) 0.1958
    R-Factor(R-Free) 0.2515
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6644
    Shell Resolution(Low) 2.7503
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2652
    R-Factor(R-Work) 0.1985
    R-Factor(R-Free) 0.2353
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7503
    Shell Resolution(Low) 2.8486
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2624
    R-Factor(R-Work) 0.2059
    R-Factor(R-Free) 0.2392
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8486
    Shell Resolution(Low) 2.9626
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 2621
    R-Factor(R-Work) 0.197
    R-Factor(R-Free) 0.2609
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9626
    Shell Resolution(Low) 3.0974
    Number of Reflections(R-Free) 128
    Number of Reflections(R-Work) 2633
    R-Factor(R-Work) 0.2016
    R-Factor(R-Free) 0.2238
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0974
    Shell Resolution(Low) 3.2606
    Number of Reflections(R-Free) 124
    Number of Reflections(R-Work) 2650
    R-Factor(R-Work) 0.191
    R-Factor(R-Free) 0.2154
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2606
    Shell Resolution(Low) 3.4648
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2641
    R-Factor(R-Work) 0.1785
    R-Factor(R-Free) 0.218
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4648
    Shell Resolution(Low) 3.732
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2616
    R-Factor(R-Work) 0.1708
    R-Factor(R-Free) 0.2125
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.732
    Shell Resolution(Low) 4.1072
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2629
    R-Factor(R-Work) 0.1587
    R-Factor(R-Free) 0.1838
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1072
    Shell Resolution(Low) 4.7006
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 2634
    R-Factor(R-Work) 0.1552
    R-Factor(R-Free) 0.2
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7006
    Shell Resolution(Low) 5.9185
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2635
    R-Factor(R-Work) 0.177
    R-Factor(R-Free) 0.1984
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.9185
    Shell Resolution(Low) 37.663
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2707
    R-Factor(R-Work) 0.1864
    R-Factor(R-Free) 0.1908
    Percent Reflections(Observed) 95.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 15.721
    f_plane_restr 0.004
    f_chiral_restr 0.07
    f_angle_d 1.002
    f_bond_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 7495
    Nucleic Acid Atoms 481
    Heterogen Atoms 58
    Solvent Atoms 496
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHASES
    Structure Refinement PHENIX (phenix.refine: 1.7.2_869)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction SCALEPACK