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An Information Portal to 105025 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4KXT
  •   Crystallization Hide
    Crystallization Experiments
    Method EVAPORATION
    pH 8
    Temperature 293.0
    Details 50 mM Tris-HCl pH 8.0, 50 mM sodium chloride, 5 mM magnesium chloride, 1 mM dithiothreitol, 50% glycerol, EVAPORATION, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 69.88 α = 90
    b = 100.25 β = 90
    c = 136.7 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 AREA DETECTOR
    Type DECTRIS PILATUS 6M
    Collection Date 2013-04-15
     
    Diffraction Radiation
    Monochromator Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 24-ID-E
    Wavelength List 0.97920
    Site APS
    Beamline 24-ID-E
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 3.0
    Observed Criterion Sigma(I) 3.0
    Resolution(High) 2.29
    Resolution(Low) 50
    Number Reflections(Observed) 43638
    Percent Possible(Observed) 99.9
     
    High Resolution Shell Details
    Resolution(High) 2.294
    Resolution(Low) 2.38
    Percent Possible(All) 99.6
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.294
    Resolution(Low) 48.863
    Cut-off Sigma(F) 1.36
    Number of Reflections(all) 43638
    Number of Reflections(Observed) 43565
    Number of Reflections(R-Free) 2000
    Percent Reflections(Observed) 99.53
    R-Factor(Observed) 0.1774
    R-Work 0.175
    R-Free 0.2282
     
    Temperature Factor Modeling
    Data Not Available
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.294
    Shell Resolution(Low) 2.3512
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2778
    R-Factor(R-Work) 0.2117
    R-Factor(R-Free) 0.2795
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3512
    Shell Resolution(Low) 2.4147
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2937
    R-Factor(R-Work) 0.1919
    R-Factor(R-Free) 0.2678
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4147
    Shell Resolution(Low) 2.4858
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2929
    R-Factor(R-Work) 0.1989
    R-Factor(R-Free) 0.2578
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4858
    Shell Resolution(Low) 2.566
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2947
    R-Factor(R-Work) 0.1888
    R-Factor(R-Free) 0.2709
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.566
    Shell Resolution(Low) 2.6577
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2949
    R-Factor(R-Work) 0.188
    R-Factor(R-Free) 0.2545
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6577
    Shell Resolution(Low) 2.7641
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2928
    R-Factor(R-Work) 0.1949
    R-Factor(R-Free) 0.2575
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7641
    Shell Resolution(Low) 2.8899
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2958
    R-Factor(R-Work) 0.1939
    R-Factor(R-Free) 0.264
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8899
    Shell Resolution(Low) 3.0422
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2984
    R-Factor(R-Work) 0.2009
    R-Factor(R-Free) 0.3065
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0422
    Shell Resolution(Low) 3.2328
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2952
    R-Factor(R-Work) 0.1902
    R-Factor(R-Free) 0.2642
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2328
    Shell Resolution(Low) 3.4824
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2988
    R-Factor(R-Work) 0.1883
    R-Factor(R-Free) 0.2258
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4824
    Shell Resolution(Low) 3.8327
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2994
    R-Factor(R-Work) 0.1661
    R-Factor(R-Free) 0.2361
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8327
    Shell Resolution(Low) 4.387
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 3005
    R-Factor(R-Work) 0.1449
    R-Factor(R-Free) 0.195
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.387
    Shell Resolution(Low) 5.5259
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 3039
    R-Factor(R-Work) 0.1473
    R-Factor(R-Free) 0.1863
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.5259
    Shell Resolution(Low) 48.8736
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 3177
    R-Factor(R-Work) 0.1841
    R-Factor(R-Free) 0.1999
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.005
    f_chiral_restr 0.078
    f_dihedral_angle_d 15.565
    f_angle_d 1.165
    f_bond_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 6473
    Nucleic Acid Atoms 222
    Heterogen Atoms 0
    Solvent Atoms 288
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution Phaser-MR
    Structure Refinement PHENIX (phenix.refine: 1.8.2_1309)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.8.2_1309)
    model building Phaser-MR
    data collection HKL-2000