POP-OUT | CLOSE
 
X-RAY DIFFRACTION
Materials and Methods page
4I7P
  •   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 = 48.37 α = 90
    b = 75.4 β = 93.32
    c = 52.7 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) 1.6
    Resolution(Low) 48.29
    Number Reflections(Observed) 48062
    Percent Possible(Observed) 95.9
    R Merge I(Observed) 0.066
    B(Isotropic) From Wilson Plot 19.275
     
    High Resolution Shell Details
    Resolution(High) 1.6
    Resolution(Low) 1.69
    Percent Possible(All) 98.3
    R Merge I(Observed) 0.365
    Mean I Over Sigma(Observed) 3.1
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.6
    Resolution(Low) 48.289
    Cut-off Sigma(F) 1.99
    Number of Reflections(Observed) 48060
    Number of Reflections(R-Free) 1918
    Percent Reflections(Observed) 96.5
    R-Factor(Observed) 0.1804
    R-Work 0.1794
    R-Free 0.2042
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 14.667
    Anisotropic B[1][1] -1.7287
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -0.0993
    Anisotropic B[2][2] 1.0666
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.662
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6
    Shell Resolution(Low) 1.64
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 3322
    R-Factor(R-Work) 0.2309
    R-Factor(R-Free) 0.2431
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.64
    Shell Resolution(Low) 1.6844
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 3326
    R-Factor(R-Work) 0.2185
    R-Factor(R-Free) 0.2311
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6844
    Shell Resolution(Low) 1.7339
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 3359
    R-Factor(R-Work) 0.1949
    R-Factor(R-Free) 0.2465
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7339
    Shell Resolution(Low) 1.7899
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 3313
    R-Factor(R-Work) 0.1926
    R-Factor(R-Free) 0.2363
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7899
    Shell Resolution(Low) 1.8539
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 3331
    R-Factor(R-Work) 0.1787
    R-Factor(R-Free) 0.196
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8539
    Shell Resolution(Low) 1.9281
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 3329
    R-Factor(R-Work) 0.1704
    R-Factor(R-Free) 0.1936
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9281
    Shell Resolution(Low) 2.0159
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 3314
    R-Factor(R-Work) 0.1726
    R-Factor(R-Free) 0.2144
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0159
    Shell Resolution(Low) 2.1221
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 3318
    R-Factor(R-Work) 0.1667
    R-Factor(R-Free) 0.2089
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1221
    Shell Resolution(Low) 2.2551
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 3295
    R-Factor(R-Work) 0.1709
    R-Factor(R-Free) 0.2015
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2551
    Shell Resolution(Low) 2.4292
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 3324
    R-Factor(R-Work) 0.1722
    R-Factor(R-Free) 0.1901
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4292
    Shell Resolution(Low) 2.6737
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 3278
    R-Factor(R-Work) 0.1796
    R-Factor(R-Free) 0.2169
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6737
    Shell Resolution(Low) 3.0605
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 3254
    R-Factor(R-Work) 0.1868
    R-Factor(R-Free) 0.2082
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0605
    Shell Resolution(Low) 3.8556
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 3213
    R-Factor(R-Work) 0.1682
    R-Factor(R-Free) 0.184
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8556
    Shell Resolution(Low) 48.3109
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 3166
    R-Factor(R-Work) 0.176
    R-Factor(R-Free) 0.1885
    Percent Reflections(Observed) 91.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 13.096
    f_plane_restr 0.007
    f_chiral_restr 0.085
    f_angle_d 1.396
    f_bond_d 0.013
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2768
    Nucleic Acid Atoms 0
    Heterogen Atoms 81
    Solvent Atoms 285
     
     
  •   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