POP-OUT | CLOSE
 
X-RAY DIFFRACTION
Materials and Methods page
4ILK
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion, sitting drop
    pH 8.5
    Temperature 282.0
    Details Protein solution was at 10 mg/mL containing 20 mM Tris (pH 7.5), 100 mM NaCl and 50 mM imidazole. Mother liqueur contained 0.2 M ammonium chloride, 0.01 M calcium chloride dihydrate, 0.05 M Tris (pH 8.5), 30% PEG 4,000. Cryoprotectant was 13% glycerol, vapor diffusion, sitting drop, temperature 282K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 47.32 α = 90
    b = 97.13 β = 90
    c = 144.1 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type RAYONIX MX-225
    Collection Date 2012-03-23
     
    Diffraction Radiation
    Monochromator C(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 21-ID-F
    Wavelength List 0.97872
    Site APS
    Beamline 21-ID-F
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2
    Resolution(Low) 30
    Number Reflections(All) 45647
    Number Reflections(Observed) 45465
    Percent Possible(Observed) 99.6
    R Merge I(Observed) 0.088
    Redundancy 7.6
     
    High Resolution Shell Details
    Resolution(High) 2.0
    Resolution(Low) 2.07
    Percent Possible(All) 99.8
    R Merge I(Observed) 0.777
    Redundancy 7.1
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.003
    Resolution(Low) 29.533
    Cut-off Sigma(F) 1.36
    Number of Reflections(all) 45600
    Number of Reflections(Observed) 41885
    Number of Reflections(R-Free) 2112
    Percent Reflections(Observed) 91.89
    R-Factor(Observed) 0.1675
    R-Work 0.1648
    R-Free 0.2177
     
    Temperature Factor Modeling
    Anisotropic B[1][1] -0.7191
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 1.4606
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.7415
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.003
    Shell Resolution(Low) 2.0496
    Number of Reflections(R-Free) 89
    Number of Reflections(R-Work) 1516
    R-Factor(R-Work) 0.1924
    R-Factor(R-Free) 0.2502
    Percent Reflections(Observed) 54.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0496
    Shell Resolution(Low) 2.1009
    Number of Reflections(R-Free) 116
    Number of Reflections(R-Work) 1836
    R-Factor(R-Work) 0.1859
    R-Factor(R-Free) 0.2944
    Percent Reflections(Observed) 66.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1009
    Shell Resolution(Low) 2.1576
    Number of Reflections(R-Free) 114
    Number of Reflections(R-Work) 2274
    R-Factor(R-Work) 0.1898
    R-Factor(R-Free) 0.2539
    Percent Reflections(Observed) 79.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1576
    Shell Resolution(Low) 2.2211
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2522
    R-Factor(R-Work) 0.1719
    R-Factor(R-Free) 0.2649
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2211
    Shell Resolution(Low) 2.2928
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2709
    R-Factor(R-Work) 0.1679
    R-Factor(R-Free) 0.2202
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2928
    Shell Resolution(Low) 2.3747
    Number of Reflections(R-Free) 161
    Number of Reflections(R-Work) 2772
    R-Factor(R-Work) 0.1797
    R-Factor(R-Free) 0.2474
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3747
    Shell Resolution(Low) 2.4697
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2838
    R-Factor(R-Work) 0.1756
    R-Factor(R-Free) 0.232
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4697
    Shell Resolution(Low) 2.5821
    Number of Reflections(R-Free) 167
    Number of Reflections(R-Work) 2771
    R-Factor(R-Work) 0.1741
    R-Factor(R-Free) 0.2299
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5821
    Shell Resolution(Low) 2.7181
    Number of Reflections(R-Free) 161
    Number of Reflections(R-Work) 2864
    R-Factor(R-Work) 0.1813
    R-Factor(R-Free) 0.2709
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7181
    Shell Resolution(Low) 2.8883
    Number of Reflections(R-Free) 123
    Number of Reflections(R-Work) 2893
    R-Factor(R-Work) 0.1847
    R-Factor(R-Free) 0.2247
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8883
    Shell Resolution(Low) 3.111
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2895
    R-Factor(R-Work) 0.1858
    R-Factor(R-Free) 0.226
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.111
    Shell Resolution(Low) 3.4237
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2925
    R-Factor(R-Work) 0.1768
    R-Factor(R-Free) 0.2542
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4237
    Shell Resolution(Low) 3.9181
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2927
    R-Factor(R-Work) 0.1585
    R-Factor(R-Free) 0.1992
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9181
    Shell Resolution(Low) 4.9327
    Number of Reflections(R-Free) 161
    Number of Reflections(R-Work) 2952
    R-Factor(R-Work) 0.13
    R-Factor(R-Free) 0.1713
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9327
    Shell Resolution(Low) 29.536
    Number of Reflections(R-Free) 181
    Number of Reflections(R-Work) 3079
    R-Factor(R-Work) 0.1536
    R-Factor(R-Free) 0.1928
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.005
    f_chiral_restr 0.075
    f_dihedral_angle_d 15.668
    f_angle_d 1.172
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 5100
    Nucleic Acid Atoms 0
    Heterogen Atoms 92
    Solvent Atoms 387
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.7.3_928)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    molecular replacement Phaser
    data reduction SCALEPACK
    data collection DENZO