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An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4HD8
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7
    Temperature 293.0
    Details 200 mM NaCl, 100 mM HEPES pH 7, 10% (v/v) isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 114.6 α = 90
    b = 114.6 β = 90
    c = 123.7 γ = 120
     
    Space Group
    Space Group Name:    H 3 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type RAYONIX MX-225
    Collection Date 2011-09-14
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type BESSY BEAMLINE 14.1
    Wavelength List 0.918
    Site BESSY
    Beamline 14.1
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.3
    Resolution(Low) 38.7
    Number Reflections(All) 14077
    Number Reflections(Observed) 14069
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.084
    Redundancy 6.9
     
    High Resolution Shell Details
    Resolution(High) 2.3
    Resolution(Low) 2.4
    Percent Possible(All) 99.9
    R Merge I(Observed) 0.487
    Mean I Over Sigma(Observed) 4.3
    Redundancy 7.0
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.3
    Resolution(Low) 38.74
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 14069
    Number of Reflections(R-Free) 704
    Percent Reflections(Observed) 99.88
    R-Factor(Observed) 0.1769
    R-Work 0.1736
    R-Free 0.2405
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 31.3997
    Anisotropic B[1][1] 0.31
    Anisotropic B[1][2] 0.31
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.31
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -1.0
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3
    Shell Resolution(Low) 2.36
    Number of Reflections(R-Free) 52
    Number of Reflections(R-Work) 979
    R-Factor(R-Work) 0.204
    R-Factor(R-Free) 0.339
    Percent Reflections(Observed) 99.81
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_gen_planes_refined 0.01
    r_chiral_restr 0.111
    r_dihedral_angle_4_deg 17.168
    r_dihedral_angle_3_deg 16.568
    r_dihedral_angle_2_deg 38.312
    r_dihedral_angle_1_deg 6.333
    r_angle_refined_deg 1.892
    r_bond_refined_d 0.017
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2102
    Nucleic Acid Atoms 0
    Heterogen Atoms 23
    Solvent Atoms 102
     
     
  •   Software and Computing Hide
    Computing
    Data Collection XDS
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution Molrep
    Structure Refinement REFMAC 5.7.0029
     
    Software
    refinement REFMAC
    model building Molrep
    data collection XDS