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An Information Portal to 105339 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4JKV
  •   Crystallization Hide
    Crystallization Experiments
    Method Lipidic Cubic Phase (LCP)
    pH 7.8
    Temperature 293.0
    Details 100 mM HEPES, pH 7.8, 70 mM ammonium fluoride, 32% (v/v) PEG400, 4% 8% (v/v) P400, Lipidic Cubic Phase (LCP), temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 75.44 α = 90
    b = 98.18 β = 103.27
    c = 84.29 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 MARMOSAIC 300 mm CCD
    Details mirrors
    Collection Date 2012-12
     
    Diffraction Radiation
    Monochromator double crystal
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 23-ID-D
    Wavelength List 1.0330
    Site APS
    Beamline 23-ID-D
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.45
    Resolution(Low) 50
    Number Reflections(Observed) 43797
    Percent Possible(Observed) 99.7
    R Merge I(Observed) 0.111
    B(Isotropic) From Wilson Plot 63.52
    Redundancy 5.5
     
    High Resolution Shell Details
    Resolution(High) 2.45
    Resolution(Low) 2.54
    Percent Possible(All) 99.6
    R Merge I(Observed) 0.94
    Mean I Over Sigma(Observed) 1.7
    Redundancy 4.5
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method SIRAS
    reflnsShellList 2.45
    Resolution(Low) 42.12
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 43776
    Number of Reflections(R-Free) 2202
    Percent Reflections(Observed) 99.35
    R-Factor(Observed) 0.2013
    R-Work 0.1997
    R-Free 0.2314
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 74.42
    Anisotropic B[1][1] 9.7708
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 1.3965
    Anisotropic B[2][2] -11.0598
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 1.289
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.45
    Shell Resolution(Low) 2.51
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2914
    R-Factor(R-Work) 0.2352
    R-Factor(R-Free) 0.2966
    Percent Reflections(Observed) 99.35
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    t_bond_d 0.009
    t_angle_deg 0.97
    t_omega_torsion 2.87
    t_other_torsion 3.24
     
    Coordinate Error
    Luzzati ESD(Observed) 0.402
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 7032
    Nucleic Acid Atoms 0
    Heterogen Atoms 237
    Solvent Atoms 110
     
     
  •   Software and Computing Hide
    Computing
    Data Collection Blue Ice
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHENIX.AutoSol
    Structure Refinement BUSTER 2.10.0
     
    Software
    refinement BUSTER version: 2.10.0
    model building PHENIX.AutoSol
    data collection Blue version: Ice