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X-RAY DIFFRACTION
Materials and Methods page
3U3W
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.5
    Temperature 291.15
    Details 0.16M Calcium Acetate, 0.08M Sodium Cacodylate, 8% PEG8000, 5% Glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 88.88 α = 90
    b = 71.09 β = 115.53
    c = 88.85 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type PSI PILATUS 6M
    Details cylindrical grazing incidence mirror
    Collection Date 2011-08-29
     
    Diffraction Radiation
    Monochromator liquid nitrogen cooled channel-cut silicon (Si) monochromator
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID29
    Wavelength List 0.97932
    Site ESRF
    Beamline ID29
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -1.0
    Resolution(High) 2.4
    Resolution(Low) 80.2
    Number Reflections(All) 39190
    Number Reflections(Observed) 38014
    Percent Possible(Observed) 97.0
    R Merge I(Observed) 0.095
    B(Isotropic) From Wilson Plot 45.4
    Redundancy 2.7
     
    High Resolution Shell Details
    Resolution(High) 2.4
    Resolution(Low) 2.53
    Percent Possible(All) 97.7
    R Merge I(Observed) 0.645
    Mean I Over Sigma(Observed) 1.1
    R-Sym I(Observed) 0.645
    Redundancy 2.6
    Number Unique Reflections(All) 5564
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.4
    Resolution(Low) 53.192
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 39346
    Number of Reflections(Observed) 36151
    Number of Reflections(R-Free) 1815
    Percent Reflections(Observed) 91.88
    R-Factor(Observed) 0.1816
    R-Work 0.1787
    R-Free 0.2348
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 47.6077
    Anisotropic B[1][1] 10.1832
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -7.3665
    Anisotropic B[2][2] -7.0556
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -3.1276
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4001
    Shell Resolution(Low) 2.465
    Number of Reflections(Observed) 2365
    Number of Reflections(R-Free) 119
    Number of Reflections(R-Work) 2365
    R-Factor(R-Work) 0.2341
    R-Factor(R-Free) 0.2757
    Percent Reflections(Observed) 82.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.465
    Shell Resolution(Low) 2.5375
    Number of Reflections(Observed) 2539
    Number of Reflections(R-Free) 122
    Number of Reflections(R-Work) 2539
    R-Factor(R-Work) 0.2388
    R-Factor(R-Free) 0.3421
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5375
    Shell Resolution(Low) 2.6194
    Number of Reflections(Observed) 2534
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2534
    R-Factor(R-Work) 0.2408
    R-Factor(R-Free) 0.3281
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6194
    Shell Resolution(Low) 2.713
    Number of Reflections(Observed) 2572
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2572
    R-Factor(R-Work) 0.2205
    R-Factor(R-Free) 0.2984
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.713
    Shell Resolution(Low) 2.8217
    Number of Reflections(Observed) 2596
    Number of Reflections(R-Free) 128
    Number of Reflections(R-Work) 2596
    R-Factor(R-Work) 0.212
    R-Factor(R-Free) 0.2545
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8217
    Shell Resolution(Low) 2.9501
    Number of Reflections(Observed) 2635
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2635
    R-Factor(R-Work) 0.2067
    R-Factor(R-Free) 0.2922
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9501
    Shell Resolution(Low) 3.1056
    Number of Reflections(Observed) 2600
    Number of Reflections(R-Free) 173
    Number of Reflections(R-Work) 2600
    R-Factor(R-Work) 0.1931
    R-Factor(R-Free) 0.2641
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1056
    Shell Resolution(Low) 3.3001
    Number of Reflections(Observed) 2755
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2755
    R-Factor(R-Work) 0.1727
    R-Factor(R-Free) 0.2506
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3001
    Shell Resolution(Low) 3.5549
    Number of Reflections(Observed) 2780
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 2780
    R-Factor(R-Work) 0.169
    R-Factor(R-Free) 0.2252
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5549
    Shell Resolution(Low) 3.9125
    Number of Reflections(Observed) 2684
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2684
    R-Factor(R-Work) 0.1627
    R-Factor(R-Free) 0.2207
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9125
    Shell Resolution(Low) 4.4784
    Number of Reflections(Observed) 2768
    Number of Reflections(R-Free) 166
    Number of Reflections(R-Work) 2768
    R-Factor(R-Work) 0.1439
    R-Factor(R-Free) 0.198
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4784
    Shell Resolution(Low) 5.6414
    Number of Reflections(Observed) 2745
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2745
    R-Factor(R-Work) 0.1521
    R-Factor(R-Free) 0.1981
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.6414
    Shell Resolution(Low) 53.2052
    Number of Reflections(Observed) 2763
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2763
    R-Factor(R-Work) 0.1826
    R-Factor(R-Free) 0.2087
    Percent Reflections(Observed) 93.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.003
    f_chiral_restr 0.072
    f_dihedral_angle_d 20.255
    f_angle_d 1.02
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4822
    Nucleic Acid Atoms 738
    Heterogen Atoms 2
    Solvent Atoms 255
     
     
  •   Software and Computing Hide
    Computing
    Data Collection MxCuBe
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) SCALA
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.7_650)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7_650)
    model building PHASER
    data collection MxCuBe