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X-RAY DIFFRACTION
Materials and Methods page
3OD8
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion
    pH 8.5
    Temperature 298.0
    Details 30% PEG 3350, 100 mM NaAcetate, 100 mM Tris pH 8.5, 0.1 mM TCEP, 20% ethylene glycol, vapor diffusion, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 63.22 α = 90
    b = 107.7 β = 100.2
    c = 86.14 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 ADSC QUANTUM 315r
    Collection Date 2009-09-17
     
    Diffraction Radiation
    Monochromator Double silicon(111) crystal
    Diffraction Protocol Single wavelength
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X29A
    Wavelength List 0.98
    Site NSLS
    Beamline X29A
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.4
    Resolution(Low) 50
    Number Reflections(Observed) 44580
    Percent Possible(Observed) 100.0
    R Merge I(Observed) 0.138
    Redundancy 8.3
     
    High Resolution Shell Details
    Resolution(High) 2.4
    Resolution(Low) 2.44
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.706
    Redundancy 8.4
    Number Unique Reflections(All) 2236
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method SAD
    reflnsShellList 2.4
    Resolution(Low) 42.609
    Cut-off Sigma(F) 1.35
    Number of Reflections(Observed) 44511
    Number of Reflections(R-Free) 2242
    Percent Reflections(Observed) 99.75
    R-Factor(Observed) 0.1941
    R-Work 0.1915
    R-Free 0.241
     
    Temperature Factor Modeling
    Mean Isotropic B Value 32.691
    Anisotropic B[1][1] 8.1853
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 2.4908
    Anisotropic B[2][2] -10.5909
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 2.4056
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4
    Shell Resolution(Low) 2.4824
    Number of Reflections(R-Free) 218
    Number of Reflections(R-Work) 4122
    R-Factor(R-Work) 0.2328
    R-Factor(R-Free) 0.3141
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4824
    Shell Resolution(Low) 2.5818
    Number of Reflections(R-Free) 229
    Number of Reflections(R-Work) 4234
    R-Factor(R-Work) 0.2201
    R-Factor(R-Free) 0.2574
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5818
    Shell Resolution(Low) 2.6992
    Number of Reflections(R-Free) 210
    Number of Reflections(R-Work) 4254
    R-Factor(R-Work) 0.2204
    R-Factor(R-Free) 0.282
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6992
    Shell Resolution(Low) 2.8415
    Number of Reflections(R-Free) 201
    Number of Reflections(R-Work) 4232
    R-Factor(R-Work) 0.2264
    R-Factor(R-Free) 0.3206
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8415
    Shell Resolution(Low) 3.0195
    Number of Reflections(R-Free) 236
    Number of Reflections(R-Work) 4206
    R-Factor(R-Work) 0.2252
    R-Factor(R-Free) 0.2955
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0195
    Shell Resolution(Low) 3.2526
    Number of Reflections(R-Free) 232
    Number of Reflections(R-Work) 4206
    R-Factor(R-Work) 0.1985
    R-Factor(R-Free) 0.2613
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2526
    Shell Resolution(Low) 3.5797
    Number of Reflections(R-Free) 223
    Number of Reflections(R-Work) 4253
    R-Factor(R-Work) 0.1718
    R-Factor(R-Free) 0.2345
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5797
    Shell Resolution(Low) 4.0974
    Number of Reflections(R-Free) 216
    Number of Reflections(R-Work) 4217
    R-Factor(R-Work) 0.1625
    R-Factor(R-Free) 0.2053
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0974
    Shell Resolution(Low) 5.1608
    Number of Reflections(R-Free) 234
    Number of Reflections(R-Work) 4260
    R-Factor(R-Work) 0.1422
    R-Factor(R-Free) 0.186
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1608
    Shell Resolution(Low) 42.6162
    Number of Reflections(R-Free) 243
    Number of Reflections(R-Work) 4285
    R-Factor(R-Work) 0.1624
    R-Factor(R-Free) 0.1926
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 21.43
    f_plane_restr 0.005
    f_chiral_restr 0.072
    f_angle_d 1.269
    f_bond_d 0.009
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 5697
    Nucleic Acid Atoms 1616
    Heterogen Atoms 8
    Solvent Atoms 342
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CBASS
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution SHELXS
    Structure Refinement PHENIX (phenix.refine: 1.6.1_357)
     
    Software
    data extraction pdb_extract version: 3.10
    refinement phenix
    data processing HKL