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An Information Portal to 105212 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4IKB
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion
    pH 6.5
    Temperature 293.0
    Details 0.2M ammonium sulfate, 0.1M Sodium cacodylate trihydrate pH 6.5, 30% PEG 8000, vapor diffusion, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 53.48 α = 90
    b = 38.74 β = 101.13
    c = 73.46 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   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 0.9792
    Site SSRF
    Beamline BL17U
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 1.78
    Resolution(Low) 72.07
    Number Reflections(All) 27836
    Number Reflections(Observed) 27836
    Percent Possible(Observed) 97.4
    Redundancy 5.2
     
    High Resolution Shell Details
    Resolution(High) 1.78
    Resolution(Low) 1.88
    Percent Possible(All) 96.4
    R Merge I(Observed) 0.129
    Mean I Over Sigma(Observed) 5.2
    R-Sym I(Observed) 0.129
    Redundancy 5.3
    Number Unique Reflections(All) 3973
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.78
    Resolution(Low) 34.12
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 27834
    Number of Reflections(R-Free) 1407
    Percent Reflections(Observed) 97.04
    R-Factor(Observed) 0.1713
    R-Work 0.1687
    R-Free 0.2213
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 19.4674
    Anisotropic B[1][1] 0.35
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.27
    Anisotropic B[2][2] -0.09
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.16
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.78
    Shell Resolution(Low) 1.826
    Number of Reflections(R-Free) 92
    Number of Reflections(R-Work) 1823
    R-Factor(R-Work) 0.185
    R-Factor(R-Free) 0.239
    Percent Reflections(Observed) 95.56
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_gen_planes_other 0.001
    r_gen_planes_refined 0.008
    r_chiral_restr 0.13
    r_dihedral_angle_4_deg 15.518
    r_dihedral_angle_3_deg 13.332
    r_dihedral_angle_2_deg 34.794
    r_dihedral_angle_1_deg 6.096
    r_angle_other_deg 0.942
    r_angle_refined_deg 1.732
    r_bond_other_d 0.007
    r_bond_refined_d 0.013
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2111
    Nucleic Acid Atoms 0
    Heterogen Atoms 78
    Solvent Atoms 247
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (data scaling) SCALA
    Structure Solution Balbes
    Structure Refinement REFMAC 5.6.0117
     
    Software
    data extraction pdb_extract version: 3.11
    refinement REFMAC5
    data reduction SCALA version: 3.3.20