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X-RAY DIFFRACTION
Materials and Methods page
3VD8
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 4
    Temperature 298.0
    Details 20% PEG3350, 0.1M Potassium Acetate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 61.6 α = 90
    b = 91.93 β = 90
    c = 100.28 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 300 mm CCD
    Details mirrors
    Collection Date 2011-03-07
     
    Diffraction Radiation
    Monochromator Si 111 CHANNEL
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 23-ID-B
    Wavelength List 0.9794
    Site APS
    Beamline 23-ID-B
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.07
    Resolution(Low) 50
    Number Reflections(All) 35519
    Number Reflections(Observed) 35164
    Percent Possible(Observed) 99.0
    Redundancy 7.0
     
    High Resolution Shell Details
    Resolution(High) 2.068
    Resolution(Low) 2.11
    Percent Possible(All) 97.0
    R Merge I(Observed) 0.646
    Mean I Over Sigma(Observed) 2.24
    Redundancy 6.0
    Number Unique Reflections(All) 1704
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.0685
    Resolution(Low) 38.887
    Cut-off Sigma(F) 0.82
    Number of Reflections(all) 35519
    Number of Reflections(Observed) 34906
    Number of Reflections(R-Free) 1741
    Percent Reflections(Observed) 98.33
    R-Factor(Observed) 0.1841
    R-Work 0.1821
    R-Free 0.2212
    R-Free Selection Details random
     
    Temperature Factor Modeling
    Anisotropic B[1][1] -0.233
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.1537
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.0793
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0685
    Shell Resolution(Low) 2.1293
    Number of Reflections(R-Free) 120
    Number of Reflections(R-Work) 2713
    R-Factor(R-Work) 0.2457
    R-Factor(R-Free) 0.2812
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1293
    Shell Resolution(Low) 2.198
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2693
    R-Factor(R-Work) 0.2187
    R-Factor(R-Free) 0.2838
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.198
    Shell Resolution(Low) 2.2766
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2713
    R-Factor(R-Work) 0.2034
    R-Factor(R-Free) 0.2559
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2766
    Shell Resolution(Low) 2.3677
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2741
    R-Factor(R-Work) 0.1936
    R-Factor(R-Free) 0.252
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3677
    Shell Resolution(Low) 2.4755
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 2753
    R-Factor(R-Work) 0.1899
    R-Factor(R-Free) 0.2316
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4755
    Shell Resolution(Low) 2.606
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2757
    R-Factor(R-Work) 0.1961
    R-Factor(R-Free) 0.2344
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.606
    Shell Resolution(Low) 2.7692
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2762
    R-Factor(R-Work) 0.1981
    R-Factor(R-Free) 0.2404
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7692
    Shell Resolution(Low) 2.9829
    Number of Reflections(R-Free) 158
    Number of Reflections(R-Work) 2759
    R-Factor(R-Work) 0.1963
    R-Factor(R-Free) 0.2446
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9829
    Shell Resolution(Low) 3.283
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2811
    R-Factor(R-Work) 0.1936
    R-Factor(R-Free) 0.2446
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.283
    Shell Resolution(Low) 3.7577
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2809
    R-Factor(R-Work) 0.1583
    R-Factor(R-Free) 0.1978
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7577
    Shell Resolution(Low) 4.733
    Number of Reflections(R-Free) 170
    Number of Reflections(R-Work) 2838
    R-Factor(R-Work) 0.1499
    R-Factor(R-Free) 0.1801
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.733
    Shell Resolution(Low) 38.8934
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2816
    R-Factor(R-Work) 0.1873
    R-Factor(R-Free) 0.2187
    Percent Reflections(Observed) 94.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.003
    f_chiral_restr 0.05
    f_dihedral_angle_d 11.391
    f_angle_d 0.694
    f_bond_d 0.003
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3630
    Nucleic Acid Atoms 0
    Heterogen Atoms 65
    Solvent Atoms 325
     
     
  •   Software and Computing Hide
    Computing
    Data Collection BlueIce
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution phaser
    Structure Refinement PHENIX (phenix.refine: dev_947)
     
    Software
    refinement PHENIX version: (phenix.refine: dev_947)
    model building phaser
    data collection BlueIce