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X-RAY DIFFRACTION
Materials and Methods page
2YNN
  •   Crystallization Hide
    Crystallization Experiments
    Details 0.1M HEPES PH 7.5, 0.5M AMMONIUM SULFATE, 30% V/V MPD
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 129.16 α = 90
    b = 129.16 β = 90
    c = 60.03 γ = 120
     
    Space Group
    Space Group Name:    P 61
     
     
  •   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) 1.73
    Resolution(Low) 56
    Number Reflections(Observed) 54637
    Percent Possible(Observed) 100.0
    R Merge I(Observed) 0.13
    B(Isotropic) From Wilson Plot 14.12
    Redundancy 2.0
     
    High Resolution Shell Details
    Resolution(High) 1.73
    Resolution(Low) 1.77
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.66
    Mean I Over Sigma(Observed) 2.7
    Redundancy 6.3
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.782
    Resolution(Low) 55.928
    Cut-off Sigma(F) 1.35
    Number of Reflections(Observed) 54637
    Number of Reflections(R-Free) 2774
    Percent Reflections(Observed) 99.96
    R-Factor(Observed) 0.163
    R-Work 0.1621
    R-Free 0.1799
     
    Temperature Factor Modeling
    Mean Isotropic B Value 14.1
    Anisotropic B[1][1] 0.4738
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.4738
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.9476
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7824
    Shell Resolution(Low) 1.8131
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2567
    R-Factor(R-Work) 0.212
    R-Factor(R-Free) 0.2289
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8131
    Shell Resolution(Low) 1.8461
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2556
    R-Factor(R-Work) 0.2037
    R-Factor(R-Free) 0.2451
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8461
    Shell Resolution(Low) 1.8816
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2579
    R-Factor(R-Work) 0.1937
    R-Factor(R-Free) 0.2243
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8816
    Shell Resolution(Low) 1.92
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2593
    R-Factor(R-Work) 0.1788
    R-Factor(R-Free) 0.2009
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.92
    Shell Resolution(Low) 1.9618
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2581
    R-Factor(R-Work) 0.1684
    R-Factor(R-Free) 0.195
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9618
    Shell Resolution(Low) 2.0074
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2575
    R-Factor(R-Work) 0.1626
    R-Factor(R-Free) 0.1766
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0074
    Shell Resolution(Low) 2.0576
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2563
    R-Factor(R-Work) 0.1597
    R-Factor(R-Free) 0.1857
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0576
    Shell Resolution(Low) 2.1133
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2575
    R-Factor(R-Work) 0.1613
    R-Factor(R-Free) 0.1966
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1133
    Shell Resolution(Low) 2.1754
    Number of Reflections(R-Free) 122
    Number of Reflections(R-Work) 2600
    R-Factor(R-Work) 0.1621
    R-Factor(R-Free) 0.1975
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1754
    Shell Resolution(Low) 2.2457
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2558
    R-Factor(R-Work) 0.1595
    R-Factor(R-Free) 0.1841
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2457
    Shell Resolution(Low) 2.3259
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2618
    R-Factor(R-Work) 0.164
    R-Factor(R-Free) 0.1962
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3259
    Shell Resolution(Low) 2.4191
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2598
    R-Factor(R-Work) 0.1582
    R-Factor(R-Free) 0.2025
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4191
    Shell Resolution(Low) 2.5292
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2575
    R-Factor(R-Work) 0.1687
    R-Factor(R-Free) 0.1799
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5292
    Shell Resolution(Low) 2.6625
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 2586
    R-Factor(R-Work) 0.173
    R-Factor(R-Free) 0.1998
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6625
    Shell Resolution(Low) 2.8293
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2604
    R-Factor(R-Work) 0.1681
    R-Factor(R-Free) 0.171
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8293
    Shell Resolution(Low) 3.0477
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2606
    R-Factor(R-Work) 0.1662
    R-Factor(R-Free) 0.1897
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0477
    Shell Resolution(Low) 3.3544
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2610
    R-Factor(R-Work) 0.163
    R-Factor(R-Free) 0.1912
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3544
    Shell Resolution(Low) 3.8397
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2616
    R-Factor(R-Work) 0.1431
    R-Factor(R-Free) 0.165
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8397
    Shell Resolution(Low) 4.8372
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2616
    R-Factor(R-Work) 0.1284
    R-Factor(R-Free) 0.1164
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8372
    Shell Resolution(Low) 55.9554
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2687
    R-Factor(R-Work) 0.1746
    R-Factor(R-Free) 0.1756
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.006
    f_chiral_restr 0.09
    f_dihedral_angle_d 12.817
    f_angle_d 1.206
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2478
    Nucleic Acid Atoms 0
    Heterogen Atoms 15
    Solvent Atoms 231
     
     
  •   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