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X-RAY DIFFRACTION
Materials and Methods page
3UMO
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion, hanging drop
    pH 4.75
    Temperature 291.0
    Details 23% PEG 4000, 0.1 M SODIUM ACETATE PH 4.75, 0.2 M AMMONIUM ACETATE, vapor diffusion, hanging drop, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 43.81 α = 90
    b = 88.77 β = 90
    c = 176.12 γ = 90
     
    Space Group
    Space Group Name:    P 2 2 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector PIXEL
    Type PSI PILATUS 6M
    Details DCM Si(311) and Si(111)
    Collection Date 2010-09-09
     
    Diffraction Radiation
    Monochromator SI(311) AND SI(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID29
    Wavelength List 0.97627
    Site ESRF
    Beamline ID29
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 2.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.7
    Resolution(Low) 50
    Number Reflections(All) 77204
    Number Reflections(Observed) 76251
    Percent Possible(Observed) 98.8
    R Merge I(Observed) 0.051
    B(Isotropic) From Wilson Plot 34.02
     
    High Resolution Shell Details
    Resolution(High) 1.696
    Resolution(Low) 1.8
    Percent Possible(All) 98.1
    R Merge I(Observed) 0.59
    Mean I Over Sigma(Observed) 2.04
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.696
    Resolution(Low) 48.967
    Cut-off Sigma(F) 2.02
    Number of Reflections(all) 77204
    Number of Reflections(Observed) 76249
    Number of Reflections(R-Free) 3813
    Percent Reflections(Observed) 98.77
    R-Factor(Observed) 0.1828
    R-Work 0.1814
    R-Free 0.2079
    R-Free Selection Details Random
     
    Temperature Factor Modeling
    Mean Isotropic B Value 30.7992
    Anisotropic B[1][1] -1.8126
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 2.0555
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.2429
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.696
    Shell Resolution(Low) 1.7177
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 2454
    R-Factor(R-Work) 0.3052
    R-Factor(R-Free) 0.3374
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7177
    Shell Resolution(Low) 1.7403
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2717
    R-Factor(R-Work) 0.2979
    R-Factor(R-Free) 0.3697
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7403
    Shell Resolution(Low) 1.7641
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2646
    R-Factor(R-Work) 0.2791
    R-Factor(R-Free) 0.3005
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7641
    Shell Resolution(Low) 1.7893
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2639
    R-Factor(R-Work) 0.2716
    R-Factor(R-Free) 0.2931
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7893
    Shell Resolution(Low) 1.816
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2701
    R-Factor(R-Work) 0.2648
    R-Factor(R-Free) 0.2947
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.816
    Shell Resolution(Low) 1.8444
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2656
    R-Factor(R-Work) 0.2584
    R-Factor(R-Free) 0.2982
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8444
    Shell Resolution(Low) 1.8746
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2637
    R-Factor(R-Work) 0.2399
    R-Factor(R-Free) 0.2784
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8746
    Shell Resolution(Low) 1.907
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2744
    R-Factor(R-Work) 0.2246
    R-Factor(R-Free) 0.2297
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.907
    Shell Resolution(Low) 1.9416
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2639
    R-Factor(R-Work) 0.201
    R-Factor(R-Free) 0.2397
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9416
    Shell Resolution(Low) 1.979
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2705
    R-Factor(R-Work) 0.1988
    R-Factor(R-Free) 0.2294
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.979
    Shell Resolution(Low) 2.0194
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2659
    R-Factor(R-Work) 0.1961
    R-Factor(R-Free) 0.2285
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0194
    Shell Resolution(Low) 2.0633
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2683
    R-Factor(R-Work) 0.1866
    R-Factor(R-Free) 0.2127
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0633
    Shell Resolution(Low) 2.1113
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2679
    R-Factor(R-Work) 0.1868
    R-Factor(R-Free) 0.2002
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1113
    Shell Resolution(Low) 2.1641
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2647
    R-Factor(R-Work) 0.1736
    R-Factor(R-Free) 0.2001
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1641
    Shell Resolution(Low) 2.2226
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2658
    R-Factor(R-Work) 0.176
    R-Factor(R-Free) 0.208
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2226
    Shell Resolution(Low) 2.288
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2670
    R-Factor(R-Work) 0.1803
    R-Factor(R-Free) 0.2453
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.288
    Shell Resolution(Low) 2.3619
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2668
    R-Factor(R-Work) 0.1787
    R-Factor(R-Free) 0.2088
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3619
    Shell Resolution(Low) 2.4463
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2706
    R-Factor(R-Work) 0.1771
    R-Factor(R-Free) 0.2134
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4463
    Shell Resolution(Low) 2.5442
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2663
    R-Factor(R-Work) 0.1764
    R-Factor(R-Free) 0.2088
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5442
    Shell Resolution(Low) 2.66
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2680
    R-Factor(R-Work) 0.1742
    R-Factor(R-Free) 0.2189
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.66
    Shell Resolution(Low) 2.8002
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2687
    R-Factor(R-Work) 0.1829
    R-Factor(R-Free) 0.2217
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8002
    Shell Resolution(Low) 2.9756
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2688
    R-Factor(R-Work) 0.1794
    R-Factor(R-Free) 0.2176
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9756
    Shell Resolution(Low) 3.2053
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2696
    R-Factor(R-Work) 0.1864
    R-Factor(R-Free) 0.2251
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2053
    Shell Resolution(Low) 3.5278
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2720
    R-Factor(R-Work) 0.1831
    R-Factor(R-Free) 0.2039
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5278
    Shell Resolution(Low) 4.0381
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2749
    R-Factor(R-Work) 0.1596
    R-Factor(R-Free) 0.1837
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0381
    Shell Resolution(Low) 5.0867
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2730
    R-Factor(R-Work) 0.1383
    R-Factor(R-Free) 0.1446
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0867
    Shell Resolution(Low) 48.9875
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2915
    R-Factor(R-Work) 0.1761
    R-Factor(R-Free) 0.1886
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 20.15
    f_plane_restr 0.004
    f_chiral_restr 0.064
    f_angle_d 1.297
    f_bond_d 0.011
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4542
    Nucleic Acid Atoms 0
    Heterogen Atoms 130
    Solvent Atoms 568
     
     
  •   Software and Computing Hide
    Computing
    Data Collection DNA
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.7.2_869)
     
    Software
    data extraction pdb_extract version: 3.10
    refinement phenix
    density modification DM
    molecular replacement Phaser
    data reduction Xscale