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X-RAY DIFFRACTION
Materials and Methods page
4I7R
  •   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 = 48.59 α = 90
    b = 75.37 β = 93.25
    c = 52.63 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 2010-12-09
     
    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) 1.52
    Resolution(Low) 48.51
    Number Reflections(Observed) 54399
    Percent Possible(Observed) 93.4
    R Merge I(Observed) 0.043
    B(Isotropic) From Wilson Plot 20.267
     
    High Resolution Shell Details
    Resolution(High) 1.52
    Resolution(Low) 1.6
    Percent Possible(All) 97.2
    R Merge I(Observed) 0.335
    Mean I Over Sigma(Observed) 3.0
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.52
    Resolution(Low) 48.512
    Cut-off Sigma(F) 2.0
    Number of Reflections(Observed) 54399
    Number of Reflections(R-Free) 2170
    Percent Reflections(Observed) 93.4
    R-Factor(Observed) 0.1704
    R-Work 0.1695
    R-Free 0.1903
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 15.1411
    Anisotropic B[1][1] -0.8163
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 1.1031
    Anisotropic B[2][2] -0.0067
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.823
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.52
    Shell Resolution(Low) 1.5554
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 3586
    R-Factor(R-Work) 0.2246
    R-Factor(R-Free) 0.2498
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5554
    Shell Resolution(Low) 1.5943
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 3618
    R-Factor(R-Work) 0.2011
    R-Factor(R-Free) 0.2252
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5943
    Shell Resolution(Low) 1.6374
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 3577
    R-Factor(R-Work) 0.192
    R-Factor(R-Free) 0.2272
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6374
    Shell Resolution(Low) 1.6856
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 3590
    R-Factor(R-Work) 0.186
    R-Factor(R-Free) 0.2348
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6856
    Shell Resolution(Low) 1.74
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 3565
    R-Factor(R-Work) 0.1719
    R-Factor(R-Free) 0.204
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.74
    Shell Resolution(Low) 1.8022
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 3583
    R-Factor(R-Work) 0.1727
    R-Factor(R-Free) 0.2124
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8022
    Shell Resolution(Low) 1.8743
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 3515
    R-Factor(R-Work) 0.167
    R-Factor(R-Free) 0.2136
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8743
    Shell Resolution(Low) 1.9596
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 3511
    R-Factor(R-Work) 0.1727
    R-Factor(R-Free) 0.2232
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9596
    Shell Resolution(Low) 2.0629
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 3485
    R-Factor(R-Work) 0.1615
    R-Factor(R-Free) 0.1964
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0629
    Shell Resolution(Low) 2.1922
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 3513
    R-Factor(R-Work) 0.158
    R-Factor(R-Free) 0.1909
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1922
    Shell Resolution(Low) 2.3614
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 3421
    R-Factor(R-Work) 0.1648
    R-Factor(R-Free) 0.179
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3614
    Shell Resolution(Low) 2.5991
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 3372
    R-Factor(R-Work) 0.1653
    R-Factor(R-Free) 0.2029
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5991
    Shell Resolution(Low) 2.9751
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 3344
    R-Factor(R-Work) 0.1745
    R-Factor(R-Free) 0.1866
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9751
    Shell Resolution(Low) 3.7481
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 3299
    R-Factor(R-Work) 0.1656
    R-Factor(R-Free) 0.17
    Percent Reflections(Observed) 88.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7481
    Shell Resolution(Low) 48.5365
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 3250
    R-Factor(R-Work) 0.1573
    R-Factor(R-Free) 0.1481
    Percent Reflections(Observed) 85.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 12.94
    f_plane_restr 0.006
    f_chiral_restr 0.078
    f_angle_d 1.272
    f_bond_d 0.01
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2752
    Nucleic Acid Atoms 0
    Heterogen Atoms 86
    Solvent Atoms 335
     
     
  •   Software and Computing Hide
    Computing
    Data Collection BLU-ICE
    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