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An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4IJK
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION
    Temperature 289.0
    Details 0.2 M sodium fluoride, 22.5% PEG3350, VAPOR DIFFUSION, temperature 289K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 127.17 α = 90
    b = 114.64 β = 90
    c = 69.5 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Details MIRRORS
    Collection Date 2012-11-11
     
    Diffraction Radiation
    Monochromator Rosenbaum-Rock high-resolution double-crystal Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 19-ID
    Wavelength List 0.9792
    Site APS
    Beamline 19-ID
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.54
    Resolution(Low) 50
    Number Reflections(Observed) 33838
    Percent Possible(Observed) 98.9
    R Merge I(Observed) 0.108
    B(Isotropic) From Wilson Plot 34.9
    Redundancy 5.0
     
    High Resolution Shell Details
    Resolution(High) 2.54
    Resolution(Low) 2.58
    Percent Possible(All) 97.2
    R Merge I(Observed) 0.571
    Mean I Over Sigma(Observed) 2.3
    Redundancy 4.6
    Number Unique Reflections(All) 1632
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.54
    Resolution(Low) 46.96
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 31612
    Number of Reflections(R-Free) 1606
    Percent Reflections(Observed) 92.48
    R-Factor(Observed) 0.2366
    R-Work 0.2347
    R-Free 0.2723
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 27.2763
    Anisotropic B[1][1] -1.71
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 3.02
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -1.31
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.54
    Shell Resolution(Low) 2.608
    Number of Reflections(R-Free) 70
    Number of Reflections(R-Work) 1337
    R-Factor(R-Work) 0.26
    R-Factor(R-Free) 0.292
    Percent Reflections(Observed) 57.26
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_gen_planes_other 0.006
    r_gen_planes_refined 0.008
    r_chiral_restr 0.07
    r_dihedral_angle_4_deg 15.009
    r_dihedral_angle_3_deg 15.59
    r_dihedral_angle_2_deg 36.453
    r_dihedral_angle_1_deg 5.963
    r_angle_other_deg 1.184
    r_angle_refined_deg 1.356
    r_bond_other_d 0.007
    r_bond_refined_d 0.013
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 6787
    Nucleic Acid Atoms 0
    Heterogen Atoms 1
    Solvent Atoms 94
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) HKL3000
    Data Reduction (data scaling) HKL3000
    Structure Solution MOLREP
    Structure Refinement REFMAC 5.7.0029
     
    Software
    data extraction pdb_extract version: 3.11
    refinement REFMAC5
    molecular replacement MOLREP
    data reduction HKL