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X-RAY DIFFRACTION
Materials and Methods page
4EC5
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 7.5
    Temperature 293.15
    Details 0.1M HEPES pH 7.5, 14% PEG8000, 0.2M Calcium acetate hydrate, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 120.79 α = 90
    b = 39.78 β = 99.75
    c = 93.9 γ = 90
     
    Space Group
    Space Group Name:    C 1 2 1
     
     
  •   Diffraction Hide
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID23-1
    Wavelength List 0.8726
    Site ESRF
    Beamline ID23-1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 2.0
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 2.2
    Resolution(Low) 50
    Number Reflections(All) 22844
    Number Reflections(Observed) 22248
    Percent Possible(Observed) 97.4
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.197
    Resolution(Low) 46.602
    Cut-off Sigma(F) 1.99
    Number of Reflections(all) 22844
    Number of Reflections(Observed) 22245
    Number of Reflections(R-Free) 1117
    Percent Reflections(Observed) 97.41
    R-Factor(Observed) 0.2141
    R-Work 0.213
    R-Free 0.2338
    R-Free Selection Details 5% of total reflections, using the Rfree-flag generation in phenix
     
    Temperature Factor Modeling
    Anisotropic B[1][1] 1.5957
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 1.8794
    Anisotropic B[2][2] 1.4241
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -3.0198
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.197
    Shell Resolution(Low) 2.2974
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2550
    R-Factor(R-Work) 0.2603
    R-Factor(R-Free) 0.3363
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2974
    Shell Resolution(Low) 2.4185
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2610
    R-Factor(R-Work) 0.2538
    R-Factor(R-Free) 0.3089
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4185
    Shell Resolution(Low) 2.57
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2618
    R-Factor(R-Work) 0.2398
    R-Factor(R-Free) 0.2807
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.57
    Shell Resolution(Low) 2.7684
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2667
    R-Factor(R-Work) 0.2294
    R-Factor(R-Free) 0.2775
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7684
    Shell Resolution(Low) 3.0469
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2652
    R-Factor(R-Work) 0.2219
    R-Factor(R-Free) 0.2371
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0469
    Shell Resolution(Low) 3.4877
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2648
    R-Factor(R-Work) 0.2229
    R-Factor(R-Free) 0.2493
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4877
    Shell Resolution(Low) 4.3936
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2668
    R-Factor(R-Work) 0.1856
    R-Factor(R-Free) 0.1897
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3936
    Shell Resolution(Low) 46.6121
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2715
    R-Factor(R-Work) 0.192
    R-Factor(R-Free) 0.189
    Percent Reflections(Observed) 96.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.004
    f_chiral_restr 0.079
    f_dihedral_angle_d 14.148
    f_angle_d 1.165
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3089
    Nucleic Acid Atoms 0
    Heterogen Atoms 1
    Solvent Atoms 141
     
     
  •   Software and Computing Hide
    Computing
    Data Collection DNA
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) Xscale
    Structure Solution none
    Structure Refinement PHENIX (phenix.refine: 1.7.3_928)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7.3_928)
    model building none
    data collection DNA