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An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4IKD
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion
    pH 7.5
    Temperature 293.0
    Details 0.1M HEPES pH 7.5, 20% PEG 8000, vapor diffusion, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 40.12 α = 90
    b = 62.4 β = 90
    c = 66.06 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 225 mm CCD
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRF BEAMLINE BL17U
    Wavelength List 0.9791
    Site SSRF
    Beamline BL17U
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 1.6
    Resolution(Low) 45.36
    Number Reflections(All) 22474
    Number Reflections(Observed) 22474
    Percent Possible(Observed) 99.7
    Redundancy 4.2
     
    High Resolution Shell Details
    Resolution(High) 1.6
    Resolution(Low) 1.69
    Percent Possible(All) 99.8
    R Merge I(Observed) 0.521
    Mean I Over Sigma(Observed) 1.4
    R-Sym I(Observed) 0.521
    Redundancy 4.2
    Number Unique Reflections(All) 3254
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.6
    Resolution(Low) 34.29
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 22322
    Number of Reflections(R-Free) 1142
    Percent Reflections(Observed) 99.03
    R-Factor(Observed) 0.1885
    R-Work 0.186
    R-Free 0.2374
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 24.3801
    Anisotropic B[1][1] -0.35
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.76
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.41
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6
    Shell Resolution(Low) 1.641
    Number of Reflections(R-Free) 66
    Number of Reflections(R-Work) 1425
    R-Factor(R-Work) 0.276
    R-Factor(R-Free) 0.332
    Percent Reflections(Observed) 99.67
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_gen_planes_other 0.001
    r_gen_planes_refined 0.009
    r_chiral_restr 0.112
    r_dihedral_angle_4_deg 15.037
    r_dihedral_angle_3_deg 15.095
    r_dihedral_angle_2_deg 31.183
    r_dihedral_angle_1_deg 5.835
    r_angle_other_deg 0.965
    r_angle_refined_deg 1.751
    r_bond_other_d 0.001
    r_bond_refined_d 0.015
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1214
    Nucleic Acid Atoms 0
    Heterogen Atoms 7
    Solvent Atoms 158
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (data scaling) SCALA
    Structure Solution MOLREP
    Structure Refinement REFMAC 5.6.0117
     
    Software
    data extraction pdb_extract version: 3.11
    refinement REFMAC5
    molecular replacement MOLREP
    data reduction SCALA version: 3.3.20