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X-RAY DIFFRACTION
Materials and Methods page
3VAD
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.5
    Temperature 293.0
    Details 12% PEG8000, 0.1 M Tris, 1.9 M NaCl, 250mM KCl, 400mM Arg-HCl,2mM MgCl2, 5% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 128.08 α = 90
    b = 128.08 β = 90
    c = 74.04 γ = 90
     
    Space Group
    Space Group Name:    P 42 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315r
    Collection Date 2011-10-21
     
    Diffraction Radiation
    Monochromator double-crystal
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 19-ID
    Wavelength List 0.97915
    Site APS
    Beamline 19-ID
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 2.0
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 2.6
    Resolution(Low) 50
    Number Reflections(All) 19456
    Number Reflections(Observed) 19442
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.074
    Redundancy 8.4
     
    High Resolution Shell Details
    Resolution(High) 2.6
    Resolution(Low) 2.64
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.877
    Mean I Over Sigma(Observed) 2.31
    R-Sym I(Observed) 0.746
    Redundancy 8.4
    Number Unique Reflections(All) 958
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.602
    Resolution(Low) 40.502
    Cut-off Sigma(F) 0.13
    Number of Reflections(all) 19454
    Number of Reflections(Observed) 19328
    Number of Reflections(R-Free) 991
    Percent Reflections(Observed) 99.35
    R-Factor(Observed) 0.2288
    R-Work 0.2264
    R-Free 0.2761
    R-Free Selection Details random
     
    Temperature Factor Modeling
    Anisotropic B[1][1] -0.261
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.261
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.522
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6015
    Shell Resolution(Low) 2.7387
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2529
    R-Factor(R-Work) 0.2852
    R-Factor(R-Free) 0.3605
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7387
    Shell Resolution(Low) 2.9102
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2536
    R-Factor(R-Work) 0.272
    R-Factor(R-Free) 0.3672
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9102
    Shell Resolution(Low) 3.1348
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2589
    R-Factor(R-Work) 0.2513
    R-Factor(R-Free) 0.2848
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1348
    Shell Resolution(Low) 3.4502
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2592
    R-Factor(R-Work) 0.2419
    R-Factor(R-Free) 0.3096
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4502
    Shell Resolution(Low) 3.949
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2603
    R-Factor(R-Work) 0.2259
    R-Factor(R-Free) 0.2581
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.949
    Shell Resolution(Low) 4.9739
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2661
    R-Factor(R-Work) 0.1996
    R-Factor(R-Free) 0.2459
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9739
    Shell Resolution(Low) 40.507
    Number of Reflections(R-Free) 121
    Number of Reflections(R-Work) 2827
    R-Factor(R-Work) 0.2209
    R-Factor(R-Free) 0.2616
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.005
    f_chiral_restr 0.085
    f_dihedral_angle_d 16.183
    f_angle_d 1.37
    f_bond_d 0.011
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2505
    Nucleic Acid Atoms 0
    Heterogen Atoms 57
    Solvent Atoms 2
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHENIX (phenix.refine: 1.7.1_743)
    Structure Refinement PHENIX (phenix.refine: 1.7.1_743)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7.1_743)
    model building PHENIX version: (phenix.refine: 1.7.1_743)
    data collection HKL-2000