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X-RAY DIFFRACTION
Materials and Methods page
4I7M
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion, hanging drop
    pH 4.5
    Temperature 277.0
    Details 0.1 M sodium acetate, pH 4.5, 30% (w/v) PEG-6000, 0.3 M LiSO4, 3% (w/v) TMAO, 50 mM 2-mercaptoethanol, 50 mM 2-hydroxyethyl disulfide, vapor diffusion, hanging drop, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 48.3 α = 90
    b = 75.09 β = 93.08
    c = 52.76 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 2012-06-02
     
    Diffraction Radiation
    Monochromator two flat Si(111) crystals, mounted in a model DCM from Khozu
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ALS BEAMLINE 8.3.1
    Wavelength List 1.116
    Site ALS
    Beamline 8.3.1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.48
    Resolution(Low) 43.13
    Number Reflections(Observed) 60993
    Percent Possible(Observed) 97.4
    R Merge I(Observed) 0.053
    B(Isotropic) From Wilson Plot 21.865
     
    High Resolution Shell Details
    Resolution(High) 1.48
    Resolution(Low) 1.56
    Percent Possible(All) 99.4
    R Merge I(Observed) 0.47
    Mean I Over Sigma(Observed) 2.24
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.48
    Resolution(Low) 43.128
    Cut-off Sigma(F) 1.99
    Number of Reflections(Observed) 60991
    Number of Reflections(R-Free) 2437
    Percent Reflections(Observed) 97.39
    R-Factor(Observed) 0.1753
    R-Work 0.1743
    R-Free 0.1981
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 18.8111
    Anisotropic B[1][1] 0.1971
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 1.0694
    Anisotropic B[2][2] 0.3903
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.5875
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.48
    Shell Resolution(Low) 1.5102
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 3515
    R-Factor(R-Work) 0.2378
    R-Factor(R-Free) 0.273
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5102
    Shell Resolution(Low) 1.5431
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 3486
    R-Factor(R-Work) 0.2228
    R-Factor(R-Free) 0.2393
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5431
    Shell Resolution(Low) 1.579
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 3498
    R-Factor(R-Work) 0.2098
    R-Factor(R-Free) 0.2476
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.579
    Shell Resolution(Low) 1.6184
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 3505
    R-Factor(R-Work) 0.2019
    R-Factor(R-Free) 0.2367
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6184
    Shell Resolution(Low) 1.6622
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 3503
    R-Factor(R-Work) 0.1896
    R-Factor(R-Free) 0.2207
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6622
    Shell Resolution(Low) 1.7111
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 3468
    R-Factor(R-Work) 0.1836
    R-Factor(R-Free) 0.2164
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7111
    Shell Resolution(Low) 1.7663
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 3467
    R-Factor(R-Work) 0.1824
    R-Factor(R-Free) 0.2238
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7663
    Shell Resolution(Low) 1.8295
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 3495
    R-Factor(R-Work) 0.1731
    R-Factor(R-Free) 0.2366
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8295
    Shell Resolution(Low) 1.9027
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 3455
    R-Factor(R-Work) 0.1671
    R-Factor(R-Free) 0.1937
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9027
    Shell Resolution(Low) 1.9893
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 3486
    R-Factor(R-Work) 0.1655
    R-Factor(R-Free) 0.1936
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9893
    Shell Resolution(Low) 2.0942
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 3452
    R-Factor(R-Work) 0.1659
    R-Factor(R-Free) 0.1962
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0942
    Shell Resolution(Low) 2.2254
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 3451
    R-Factor(R-Work) 0.1619
    R-Factor(R-Free) 0.1901
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2254
    Shell Resolution(Low) 2.3972
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 3400
    R-Factor(R-Work) 0.1598
    R-Factor(R-Free) 0.2164
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3972
    Shell Resolution(Low) 2.6384
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 3355
    R-Factor(R-Work) 0.168
    R-Factor(R-Free) 0.2034
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6384
    Shell Resolution(Low) 3.0201
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 3340
    R-Factor(R-Work) 0.1805
    R-Factor(R-Free) 0.1859
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0201
    Shell Resolution(Low) 3.8047
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 3344
    R-Factor(R-Work) 0.1643
    R-Factor(R-Free) 0.1819
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8047
    Shell Resolution(Low) 43.146
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 3334
    R-Factor(R-Work) 0.171
    R-Factor(R-Free) 0.1666
    Percent Reflections(Observed) 92.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 13.312
    f_plane_restr 0.01
    f_chiral_restr 0.124
    f_angle_d 1.849
    f_bond_d 0.021
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2735
    Nucleic Acid Atoms 0
    Heterogen Atoms 82
    Solvent Atoms 298
     
     
  •   Software and Computing Hide
    Computing
    Data Collection BLU-IICE
    Data Reduction (intensity integration) XSCALE
    Data Reduction (data scaling) XSCALE
    Structure Solution PHENIX
    Structure Refinement PHENIX (phenix.refine: 1.7.1_743)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction Xscale