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X-RAY DIFFRACTION
Materials and Methods page
4K8Z
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 8
    Temperature 291.0
    Details 50mM Na-Cacodylate, 20mM MgCl2, 1mM Cobalt(III)-hexamminechloride, 1mM Spermine, 20%v/v 2-propanol, , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 144.87 α = 90
    b = 111.78 β = 90
    c = 67.1 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector PIXEL
    Type PSI PILATUS 6M
    Details LN2 cooled fixed-exit Si(111) monochromator Dynamically bendable mirror
    Collection Date 2012-06-28
     
    Diffraction Radiation
    Monochromator LN2 cooled fixed-exit Si(111) monochromator
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SLS BEAMLINE X06SA
    Wavelength List 1.00002
    Site SLS
    Beamline X06SA
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 1.81
    Resolution(High) 2.29
    Resolution(Low) 49.32
    Number Reflections(All) 49885
    Number Reflections(Observed) 49755
    Percent Possible(Observed) 99.7
    R Merge I(Observed) 0.135
    B(Isotropic) From Wilson Plot 43.91
    Redundancy 16.15
     
    High Resolution Shell Details
    Resolution(High) 2.29
    Resolution(Low) 2.35
    Percent Possible(All) 96.7
    R Merge I(Observed) 1.888
    Mean I Over Sigma(Observed) 1.81
    R-Sym I(Observed) 1.965
    Redundancy 13.16
    Number Unique Reflections(All) 3506
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.29
    Resolution(Low) 45.05
    Cut-off Sigma(F) 2.0
    Number of Reflections(all) 49755
    Number of Reflections(Observed) 49743
    Number of Reflections(R-Free) 2516
    Percent Reflections(Observed) 99.74
    R-Factor(All) 0.1827
    R-Factor(Observed) 0.1827
    R-Work 0.1807
    R-Free 0.2184
    R-Free Selection Details random
     
    Temperature Factor Modeling
    Mean Isotropic B Value 46.8922
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2895
    Shell Resolution(Low) 2.3335
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2482
    R-Factor(R-Work) 0.3126
    R-Factor(R-Free) 0.3623
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3335
    Shell Resolution(Low) 2.3812
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2574
    R-Factor(R-Work) 0.2618
    R-Factor(R-Free) 0.3336
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3812
    Shell Resolution(Low) 2.4329
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2607
    R-Factor(R-Work) 0.2299
    R-Factor(R-Free) 0.2692
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4329
    Shell Resolution(Low) 2.4895
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2601
    R-Factor(R-Work) 0.2203
    R-Factor(R-Free) 0.2446
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4895
    Shell Resolution(Low) 2.5518
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2561
    R-Factor(R-Work) 0.2144
    R-Factor(R-Free) 0.2659
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5518
    Shell Resolution(Low) 2.6208
    Number of Reflections(R-Free) 120
    Number of Reflections(R-Work) 2619
    R-Factor(R-Work) 0.2074
    R-Factor(R-Free) 0.2623
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6208
    Shell Resolution(Low) 2.6979
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2610
    R-Factor(R-Work) 0.2095
    R-Factor(R-Free) 0.2662
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6979
    Shell Resolution(Low) 2.785
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2607
    R-Factor(R-Work) 0.2078
    R-Factor(R-Free) 0.257
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.785
    Shell Resolution(Low) 2.8845
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2575
    R-Factor(R-Work) 0.2028
    R-Factor(R-Free) 0.2529
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8845
    Shell Resolution(Low) 2.9999
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2630
    R-Factor(R-Work) 0.203
    R-Factor(R-Free) 0.239
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9999
    Shell Resolution(Low) 3.1364
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 2628
    R-Factor(R-Work) 0.2042
    R-Factor(R-Free) 0.2328
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1364
    Shell Resolution(Low) 3.3018
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2616
    R-Factor(R-Work) 0.1982
    R-Factor(R-Free) 0.2506
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3018
    Shell Resolution(Low) 3.5086
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2622
    R-Factor(R-Work) 0.1865
    R-Factor(R-Free) 0.2747
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5086
    Shell Resolution(Low) 3.7793
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2639
    R-Factor(R-Work) 0.175
    R-Factor(R-Free) 0.2271
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7793
    Shell Resolution(Low) 4.1594
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2671
    R-Factor(R-Work) 0.1582
    R-Factor(R-Free) 0.1792
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1594
    Shell Resolution(Low) 4.7607
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2652
    R-Factor(R-Work) 0.139
    R-Factor(R-Free) 0.1742
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7607
    Shell Resolution(Low) 5.9958
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2691
    R-Factor(R-Work) 0.1605
    R-Factor(R-Free) 0.194
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.9958
    Shell Resolution(Low) 45.0589
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2842
    R-Factor(R-Work) 0.1611
    R-Factor(R-Free) 0.1696
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.003
    f_chiral_restr 0.051
    f_dihedral_angle_d 15.254
    f_angle_d 0.72
    f_bond_d 0.003
     
    Coordinate Error
    Luzzati ESD(Observed) 0.26
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 6209
    Nucleic Acid Atoms 529
    Heterogen Atoms 16
    Solvent Atoms 367
     
     
  •   Software and Computing Hide
    Computing
    Data Collection XDS
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XDS/XSCALE
    Structure Solution PHENIX
    Structure Refinement PHENIX (phenix.refine: dev_1243)
     
    Software
    refinement PHENIX version: (phenix.refine: dev_1243)
    model building PHENIX
    data collection XDS