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X-RAY DIFFRACTION
Materials and Methods page
4I1O
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.4
    Temperature 293.0
    Details 0.1 M sodium cacodylate, pH 6.4, 0.2 M magnesium chloride, 17% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 124.41 α = 90
    b = 124.41 β = 90
    c = 147.47 γ = 120
     
    Space Group
    Space Group Name:    P 31
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector PIXEL
    Type DECTRIS PILATUS 6M
    Collection Date 2012-10-09
     
    Diffraction Radiation
    Monochromator double crystal Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SLS BEAMLINE X10SA
    Wavelength List 0.9793
    Site SLS
    Beamline X10SA
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.7
    Resolution(Low) 49.16
    Number Reflections(Observed) 70034
    Percent Possible(Observed) 100.0
    R Merge I(Observed) 0.094
    B(Isotropic) From Wilson Plot 56.958
     
    High Resolution Shell Details
    Resolution(High) 2.7
    Resolution(Low) 2.8
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.717
    Mean I Over Sigma(Observed) 3.67
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.701
    Resolution(Low) 49.157
    Cut-off Sigma(F) 1.99
    Number of Reflections(Observed) 69987
    Number of Reflections(R-Free) 3499
    Percent Reflections(Observed) 99.91
    R-Factor(Observed) 0.2191
    R-Work 0.2174
    R-Free 0.2486
     
    Temperature Factor Modeling
    Mean Isotropic B Value 50.3913
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.701
    Shell Resolution(Low) 2.7377
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2620
    R-Factor(R-Work) 0.2999
    R-Factor(R-Free) 0.3708
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7377
    Shell Resolution(Low) 2.7768
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2709
    R-Factor(R-Work) 0.3134
    R-Factor(R-Free) 0.3801
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7768
    Shell Resolution(Low) 2.8183
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2630
    R-Factor(R-Work) 0.3074
    R-Factor(R-Free) 0.297
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8183
    Shell Resolution(Low) 2.8623
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2675
    R-Factor(R-Work) 0.306
    R-Factor(R-Free) 0.3312
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8623
    Shell Resolution(Low) 2.9092
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2674
    R-Factor(R-Work) 0.2858
    R-Factor(R-Free) 0.318
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9092
    Shell Resolution(Low) 2.9594
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2667
    R-Factor(R-Work) 0.2923
    R-Factor(R-Free) 0.3062
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9594
    Shell Resolution(Low) 3.0132
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2667
    R-Factor(R-Work) 0.28
    R-Factor(R-Free) 0.2861
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0132
    Shell Resolution(Low) 3.0711
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2658
    R-Factor(R-Work) 0.2773
    R-Factor(R-Free) 0.2838
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0711
    Shell Resolution(Low) 3.1338
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2656
    R-Factor(R-Work) 0.283
    R-Factor(R-Free) 0.2899
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1338
    Shell Resolution(Low) 3.2019
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2657
    R-Factor(R-Work) 0.2717
    R-Factor(R-Free) 0.3039
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2019
    Shell Resolution(Low) 3.2764
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2675
    R-Factor(R-Work) 0.2675
    R-Factor(R-Free) 0.2986
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2764
    Shell Resolution(Low) 3.3583
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2634
    R-Factor(R-Work) 0.255
    R-Factor(R-Free) 0.314
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3583
    Shell Resolution(Low) 3.4491
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2688
    R-Factor(R-Work) 0.2432
    R-Factor(R-Free) 0.2728
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4491
    Shell Resolution(Low) 3.5506
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2642
    R-Factor(R-Work) 0.2318
    R-Factor(R-Free) 0.2553
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5506
    Shell Resolution(Low) 3.6651
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2631
    R-Factor(R-Work) 0.2217
    R-Factor(R-Free) 0.2639
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6651
    Shell Resolution(Low) 3.7961
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2695
    R-Factor(R-Work) 0.2294
    R-Factor(R-Free) 0.2438
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7961
    Shell Resolution(Low) 3.948
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2641
    R-Factor(R-Work) 0.2015
    R-Factor(R-Free) 0.2614
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.948
    Shell Resolution(Low) 4.1276
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2663
    R-Factor(R-Work) 0.1816
    R-Factor(R-Free) 0.1968
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1276
    Shell Resolution(Low) 4.3451
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2657
    R-Factor(R-Work) 0.1733
    R-Factor(R-Free) 0.2063
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3451
    Shell Resolution(Low) 4.6171
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2684
    R-Factor(R-Work) 0.1721
    R-Factor(R-Free) 0.2043
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6171
    Shell Resolution(Low) 4.9733
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2670
    R-Factor(R-Work) 0.1798
    R-Factor(R-Free) 0.1952
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9733
    Shell Resolution(Low) 5.4732
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2647
    R-Factor(R-Work) 0.1907
    R-Factor(R-Free) 0.2246
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.4732
    Shell Resolution(Low) 6.2638
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2651
    R-Factor(R-Work) 0.2009
    R-Factor(R-Free) 0.252
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.2638
    Shell Resolution(Low) 7.8865
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2659
    R-Factor(R-Work) 0.2039
    R-Factor(R-Free) 0.2489
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.8865
    Shell Resolution(Low) 49.1648
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2638
    R-Factor(R-Work) 0.1715
    R-Factor(R-Free) 0.195
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.004
    f_chiral_restr 0.07
    f_dihedral_angle_d 16.984
    f_angle_d 1.057
    f_bond_d 0.014
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 13990
    Nucleic Acid Atoms 0
    Heterogen Atoms 174
    Solvent Atoms 146
     
     
  •   Software and Computing Hide
    Computing
    Data Collection XDS
    Data Reduction (intensity integration) XSCALE
    Data Reduction (data scaling) XSCALE
    Structure Solution PHASER MR
    Structure Refinement PHENIX (phenix.refine: 1.8.1_1168)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction Xscale