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X-RAY DIFFRACTION
Materials and Methods page
3WBZ
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion, sitting drop
    pH 8
    Temperature 293.0
    Details Bis-Tris propan, NaNO3, PEG3350, pH 8.0, vapor diffusion, sitting drop, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 74.83 α = 90
    b = 217.87 β = 113.68
    c = 87.24 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
    Type RAYONIX MX225HE
    Collection Date 2011-05-17
     
    Diffraction Radiation
    Monochromator Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SPRING-8 BEAMLINE BL41XU
    Wavelength List 1.0000
    Site SPRING-8
    Beamline BL41XU
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.39
    Resolution(Low) 44.01
    Number Reflections(Observed) 97820
    Percent Possible(Observed) 97.1
    R Merge I(Observed) 0.036
    B(Isotropic) From Wilson Plot 52.468
     
    High Resolution Shell Details
    Resolution(High) 2.39
    Resolution(Low) 2.54
    Percent Possible(All) 89.8
    R Merge I(Observed) 0.259
    Mean I Over Sigma(Observed) 5.19
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.392
    Resolution(Low) 42.259
    Number of Reflections(Observed) 97819
    Number of Reflections(R-Free) 3528
    Percent Reflections(Observed) 97.35
    R-Factor(Observed) 0.1773
    R-Work 0.1762
    R-Free 0.2082
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 49.2137
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.392
    Shell Resolution(Low) 2.4248
    Number of Reflections(R-Free) 116
    Number of Reflections(R-Work) 2715
    R-Factor(R-Work) 0.2275
    R-Factor(R-Free) 0.237
    Percent Reflections(Observed) 70.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4248
    Shell Resolution(Low) 2.4594
    Number of Reflections(R-Free) 120
    Number of Reflections(R-Work) 3508
    R-Factor(R-Work) 0.2167
    R-Factor(R-Free) 0.2657
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4594
    Shell Resolution(Low) 2.4962
    Number of Reflections(R-Free) 168
    Number of Reflections(R-Work) 3844
    R-Factor(R-Work) 0.2171
    R-Factor(R-Free) 0.2639
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4962
    Shell Resolution(Low) 2.5352
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 3799
    R-Factor(R-Work) 0.2166
    R-Factor(R-Free) 0.2779
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5352
    Shell Resolution(Low) 2.5767
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 3879
    R-Factor(R-Work) 0.2273
    R-Factor(R-Free) 0.2713
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5767
    Shell Resolution(Low) 2.6211
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 3843
    R-Factor(R-Work) 0.2211
    R-Factor(R-Free) 0.2841
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6211
    Shell Resolution(Low) 2.6688
    Number of Reflections(R-Free) 163
    Number of Reflections(R-Work) 3832
    R-Factor(R-Work) 0.2028
    R-Factor(R-Free) 0.269
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6688
    Shell Resolution(Low) 2.7201
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 3843
    R-Factor(R-Work) 0.2132
    R-Factor(R-Free) 0.2734
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7201
    Shell Resolution(Low) 2.7756
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 3877
    R-Factor(R-Work) 0.2042
    R-Factor(R-Free) 0.2523
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7756
    Shell Resolution(Low) 2.836
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 3824
    R-Factor(R-Work) 0.1995
    R-Factor(R-Free) 0.2691
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.836
    Shell Resolution(Low) 2.9019
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 3901
    R-Factor(R-Work) 0.2034
    R-Factor(R-Free) 0.2296
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9019
    Shell Resolution(Low) 2.9745
    Number of Reflections(R-Free) 156
    Number of Reflections(R-Work) 3846
    R-Factor(R-Work) 0.2062
    R-Factor(R-Free) 0.253
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9745
    Shell Resolution(Low) 3.0549
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 3799
    R-Factor(R-Work) 0.208
    R-Factor(R-Free) 0.2517
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0549
    Shell Resolution(Low) 3.1447
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 3853
    R-Factor(R-Work) 0.2153
    R-Factor(R-Free) 0.2835
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1447
    Shell Resolution(Low) 3.2462
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 3879
    R-Factor(R-Work) 0.2014
    R-Factor(R-Free) 0.2166
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2462
    Shell Resolution(Low) 3.3622
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 3825
    R-Factor(R-Work) 0.1949
    R-Factor(R-Free) 0.2498
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3622
    Shell Resolution(Low) 3.4967
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 3864
    R-Factor(R-Work) 0.1781
    R-Factor(R-Free) 0.1761
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4967
    Shell Resolution(Low) 3.6558
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 3865
    R-Factor(R-Work) 0.1742
    R-Factor(R-Free) 0.214
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6558
    Shell Resolution(Low) 3.8484
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 3846
    R-Factor(R-Work) 0.1666
    R-Factor(R-Free) 0.1703
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8484
    Shell Resolution(Low) 4.0894
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 3862
    R-Factor(R-Work) 0.159
    R-Factor(R-Free) 0.1915
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0894
    Shell Resolution(Low) 4.4048
    Number of Reflections(R-Free) 156
    Number of Reflections(R-Work) 3870
    R-Factor(R-Work) 0.1481
    R-Factor(R-Free) 0.1933
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4048
    Shell Resolution(Low) 4.8475
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 3837
    R-Factor(R-Work) 0.1353
    R-Factor(R-Free) 0.1628
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8475
    Shell Resolution(Low) 5.5476
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 3872
    R-Factor(R-Work) 0.1499
    R-Factor(R-Free) 0.1693
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.5476
    Shell Resolution(Low) 6.9843
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 3898
    R-Factor(R-Work) 0.1708
    R-Factor(R-Free) 0.1887
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.9843
    Shell Resolution(Low) 42.2658
    Number of Reflections(R-Free) 117
    Number of Reflections(R-Work) 3301
    R-Factor(R-Work) 0.1593
    R-Factor(R-Free) 0.1738
    Percent Reflections(Observed) 84.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 17.735
    f_plane_restr 0.006
    f_chiral_restr 0.053
    f_angle_d 1.261
    f_bond_d 0.009
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 17474
    Nucleic Acid Atoms 0
    Heterogen Atoms 520
    Solvent Atoms 365
     
     
  •   Software and Computing Hide
    Computing
    Data Collection BSS
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XDS
    Structure Solution MOLREP
    Structure Refinement PHENIX (phenix.refine: 1.8.2_1309)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction Xscale