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X-RAY DIFFRACTION
Materials and Methods page
2YNP
  •   Crystallization Hide
    Crystallization Experiments
    Details 0.1M BICINE PH 9.0, 10% MPD
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 127.25 α = 90
    b = 127.25 β = 90
    c = 59.06 γ = 120
     
    Space Group
    Space Group Name:    P 31
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 77
     
    Diffraction Detector
    Detector PIXEL (PILATUS 2M)
    Type DECTRIS
    Collection Date 2011-07-02
     
    Diffraction Radiation
    Monochromator SINGLE BOUNCE
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type DIAMOND BEAMLINE I04-1
    Wavelength 0.917
    Site DIAMOND
    Beamline I04-1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 2.96
    Resolution(Low) 63.6
    Number Reflections(Observed) 22113
    Percent Possible(Observed) 99.3
    R Merge I(Observed) 0.06
    B(Isotropic) From Wilson Plot 73.06
    Redundancy 3.7
     
    High Resolution Shell Details
    Resolution(High) 2.96
    Resolution(Low) 3.04
    Percent Possible(All) 99.9
    R Merge I(Observed) 0.57
    Mean I Over Sigma(Observed) 2.0
    Redundancy 3.8
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.962
    Resolution(Low) 63.625
    Cut-off Sigma(F) 1.98
    Number of Reflections(Observed) 22113
    Number of Reflections(R-Free) 1133
    Percent Reflections(Observed) 99.34
    R-Factor(Observed) 0.2425
    R-Work 0.2396
    R-Free 0.2943
     
    Temperature Factor Modeling
    Mean Isotropic B Value 73.1
    Anisotropic B[1][1] -5.712
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -5.712
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 11.4241
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9617
    Shell Resolution(Low) 3.0965
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2649
    R-Factor(R-Work) 0.3033
    R-Factor(R-Free) 0.3936
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0965
    Shell Resolution(Low) 3.2598
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 2674
    R-Factor(R-Work) 0.2715
    R-Factor(R-Free) 0.3615
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2598
    Shell Resolution(Low) 3.464
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2612
    R-Factor(R-Work) 0.2515
    R-Factor(R-Free) 0.3205
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.464
    Shell Resolution(Low) 3.7314
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 2638
    R-Factor(R-Work) 0.2394
    R-Factor(R-Free) 0.3299
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7314
    Shell Resolution(Low) 4.1069
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2600
    R-Factor(R-Work) 0.2384
    R-Factor(R-Free) 0.3099
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1069
    Shell Resolution(Low) 4.701
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2588
    R-Factor(R-Work) 0.2197
    R-Factor(R-Free) 0.2584
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.701
    Shell Resolution(Low) 5.9221
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2631
    R-Factor(R-Work) 0.2214
    R-Factor(R-Free) 0.2602
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.9221
    Shell Resolution(Low) 63.6397
    Number of Reflections(R-Free) 158
    Number of Reflections(R-Work) 2588
    R-Factor(R-Work) 0.2461
    R-Factor(R-Free) 0.2829
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.005
    f_chiral_restr 0.094
    f_dihedral_angle_d 16.141
    f_angle_d 1.381
    f_bond_d 0.009
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4851
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 2
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) XIA2
    Data Reduction (data scaling) SCALA
    Structure Solution PHASER
    Structure Refinement PHENIX (PHENIX.REFINE)
     
    Software
    refinement PHENIX version: (PHENIX.REFINE)
    model building PHASER