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X-RAY DIFFRACTION
Materials and Methods page
3M7D
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5
    Temperature 303.0
    Details 0.1M phospate citrate pH 5, 0.2 M NaCl, 15% PEG 3350, 8% dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 303K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 104.15 α = 90
    b = 47.74 β = 112.48
    c = 81.22 γ = 90
     
    Space Group
    Space Group Name:    C 1 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 78
     
    Diffraction Detector
    Detector CCD
    Type RAYONIX MX-225
    Collection Date 2005-10-12
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 5ID-B
    Wavelength List 0.96500
    Site APS
    Beamline 5ID-B
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 1.82
    Resolution(Low) 75.05
    Number Reflections(All) 33609
    Number Reflections(Observed) 32998
    Percent Possible(Observed) 98.3
    R Merge I(Observed) 0.046
    B(Isotropic) From Wilson Plot 18.832
    Redundancy 4.1
     
    High Resolution Shell Details
    Resolution(High) 1.815
    Resolution(Low) 1.91
    Percent Possible(All) 88.6
    R Merge I(Observed) 0.194
    Mean I Over Sigma(Observed) 6.8
    R-Sym I(Observed) 0.163
    Redundancy 3.1
    Number Unique Reflections(All) 4301
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.815
    Resolution(Low) 28.056
    Cut-off Sigma(F) 1.35
    Number of Reflections(Observed) 31317
    Number of Reflections(R-Free) 1673
    Percent Reflections(Observed) 98.2
    R-Factor(Observed) 0.1771
    R-Work 0.1748
    R-Free 0.22
    R-Free Selection Details random
     
    Temperature Factor Modeling
    Anisotropic B[1][1] -4.6395
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 1.4213
    Anisotropic B[2][2] 0.8795
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 3.76
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.815
    Shell Resolution(Low) 1.8685
    Number of Reflections(R-Free) 119
    Number of Reflections(R-Work) 2128
    R-Factor(R-Work) 0.1786
    R-Factor(R-Free) 0.2481
    Percent Reflections(Observed) 82.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8685
    Shell Resolution(Low) 1.9288
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2596
    R-Factor(R-Work) 0.199
    R-Factor(R-Free) 0.2798
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9288
    Shell Resolution(Low) 1.9977
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2636
    R-Factor(R-Work) 0.1922
    R-Factor(R-Free) 0.2575
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9977
    Shell Resolution(Low) 2.0777
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2649
    R-Factor(R-Work) 0.1782
    R-Factor(R-Free) 0.2546
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0777
    Shell Resolution(Low) 2.1722
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2630
    R-Factor(R-Work) 0.1734
    R-Factor(R-Free) 0.2179
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1722
    Shell Resolution(Low) 2.2867
    Number of Reflections(R-Free) 118
    Number of Reflections(R-Work) 2680
    R-Factor(R-Work) 0.1786
    R-Factor(R-Free) 0.2383
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2867
    Shell Resolution(Low) 2.4299
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2606
    R-Factor(R-Work) 0.1739
    R-Factor(R-Free) 0.2273
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4299
    Shell Resolution(Low) 2.6174
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2700
    R-Factor(R-Work) 0.1758
    R-Factor(R-Free) 0.2087
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6174
    Shell Resolution(Low) 2.8806
    Number of Reflections(R-Free) 163
    Number of Reflections(R-Work) 2616
    R-Factor(R-Work) 0.1916
    R-Factor(R-Free) 0.2386
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8806
    Shell Resolution(Low) 3.2968
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2666
    R-Factor(R-Work) 0.1846
    R-Factor(R-Free) 0.2078
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2968
    Shell Resolution(Low) 4.1515
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2688
    R-Factor(R-Work) 0.154
    R-Factor(R-Free) 0.1984
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1515
    Shell Resolution(Low) 28.0591
    Number of Reflections(R-Free) 169
    Number of Reflections(R-Work) 2722
    R-Factor(R-Work) 0.1555
    R-Factor(R-Free) 0.1937
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.004
    f_chiral_restr 0.065
    f_dihedral_angle_d 16.074
    f_angle_d 0.92
    f_bond_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3081
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 238
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) SCALA
    Structure Solution AMoRE
    Structure Refinement PHENIX (phenix.refine: 1.5_2)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.5_2)
    model building AMoRE