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X-RAY DIFFRACTION
Materials and Methods page
3VWB
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 4.5
    Temperature 295.0
    Details 0.1M MgCl2, 0.1M Sodium Acetate, 22% PEG400, 3%(v/v) dimethyl sulfoxide, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 57.32 α = 90
    b = 163.05 β = 90
    c = 39.57 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 CCD
    Type RAYONIX MX-225
    Collection Date 2011-08-05
     
    Diffraction Radiation
    Monochromator Bartels Monochromator Crystal Type Si (111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SLS BEAMLINE X06DA
    Wavelength List 0.97920
    Site SLS
    Beamline X06DA
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) -3.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.42
    Resolution(Low) 46.89
    Number Reflections(All) 27467
    Number Reflections(Observed) 27467
    Percent Possible(Observed) 99.8
    R Merge I(Observed) 0.067
    B(Isotropic) From Wilson Plot 46.5
    Redundancy 7.77
     
    High Resolution Shell Details
    Resolution(High) 2.42
    Resolution(Low) 2.56
    Percent Possible(All) 98.8
    R Merge I(Observed) 0.768
    Mean I Over Sigma(Observed) 2.43
    Redundancy 7.54
    Number Unique Reflections(All) 4363
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method SAD
    reflnsShellList 2.416
    Resolution(Low) 46.891
    Cut-off Sigma(F) 1.99
    Number of Reflections(all) 27467
    Number of Reflections(Observed) 27362
    Number of Reflections(R-Free) 1358
    Percent Reflections(Observed) 99.58
    R-Factor(All) 0.2371
    R-Factor(Observed) 0.2371
    R-Work 0.2353
    R-Free 0.271
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 68.9097
    Anisotropic B[1][1] 14.0
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -7.5335
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -6.4665
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4161
    Shell Resolution(Low) 2.5025
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2588
    R-Factor(R-Work) 0.3641
    R-Factor(R-Free) 0.39
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5025
    Shell Resolution(Low) 2.6027
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2605
    R-Factor(R-Work) 0.3179
    R-Factor(R-Free) 0.3614
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6027
    Shell Resolution(Low) 2.7211
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2583
    R-Factor(R-Work) 0.2906
    R-Factor(R-Free) 0.2738
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7211
    Shell Resolution(Low) 2.8646
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2638
    R-Factor(R-Work) 0.2618
    R-Factor(R-Free) 0.3229
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8646
    Shell Resolution(Low) 3.044
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2619
    R-Factor(R-Work) 0.2704
    R-Factor(R-Free) 0.3344
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.044
    Shell Resolution(Low) 3.279
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2556
    R-Factor(R-Work) 0.2418
    R-Factor(R-Free) 0.2598
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.279
    Shell Resolution(Low) 3.6088
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2594
    R-Factor(R-Work) 0.2439
    R-Factor(R-Free) 0.2875
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6088
    Shell Resolution(Low) 4.1308
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2597
    R-Factor(R-Work) 0.2245
    R-Factor(R-Free) 0.2658
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1308
    Shell Resolution(Low) 5.2033
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2613
    R-Factor(R-Work) 0.2086
    R-Factor(R-Free) 0.246
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2033
    Shell Resolution(Low) 46.8995
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2611
    R-Factor(R-Work) 0.1921
    R-Factor(R-Free) 0.224
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 27.192
    f_plane_restr 0.003
    f_chiral_restr 0.046
    f_angle_d 0.979
    f_bond_d 0.004
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 931
    Nucleic Acid Atoms 1060
    Heterogen Atoms 0
    Solvent Atoms 62
     
     
  •   Software and Computing Hide
    Computing
    Data Collection RemDAq
    Data Reduction (intensity integration) XDS package
    Data Reduction (data scaling) XDS package
    Structure Solution SHELXD, SHELXE
    Structure Refinement PHENIX (phenix.refine: 1.7.3_928)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7.3_928)
    model building SHELXE
    model building SHELXD
    data collection RemDAq