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X-RAY DIFFRACTION
Materials and Methods page
4JKB
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion
    pH 7.5
    Temperature 298.0
    Details 15% PEG 4000, 300mM MgCl2, 100mM Tris, pH 7.5, vapor diffusion, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 75.36 α = 90
    b = 78.16 β = 90
    c = 93.77 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 300 mm CCD
    Collection Date 2013-02-25
     
    Diffraction Radiation
    Monochromator Si
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type CLSI BEAMLINE 08B1-1
    Wavelength List 0.97949
    Site CLSI
    Beamline 08B1-1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 1.0
    Observed Criterion Sigma(I) 1.0
    Resolution(High) 1.3
    Resolution(Low) 50
    Number Reflections(Observed) 135702
    Percent Possible(Observed) 99.4
    R Merge I(Observed) 0.041
    Redundancy 5.5
     
    High Resolution Shell Details
    Resolution(High) 1.3
    Resolution(Low) 1.35
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.568
    Redundancy 5.4
    Number Unique Reflections(All) 13514
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.3
    Resolution(Low) 40.04
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 123935
    Number of Reflections(R-Free) 6249
    Percent Reflections(Observed) 90.53
    R-Factor(Observed) 0.1207
    R-Work 0.1194
    R-Free 0.1453
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 24.2539
    Anisotropic B[1][1] -0.24
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.15
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.39
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3
    Shell Resolution(Low) 1.332
    Number of Reflections(R-Free) 168
    Number of Reflections(R-Work) 2773
    R-Factor(R-Work) 0.126
    R-Factor(R-Free) 0.175
    Percent Reflections(Observed) 29.59
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_sphericity_bonded 14.405
    r_sphericity_free 31.477
    r_bond_refined_d 0.011
    r_bond_other_d 0.001
    r_angle_refined_deg 1.442
    r_angle_other_deg 0.764
    r_dihedral_angle_1_deg 5.788
    r_dihedral_angle_2_deg 39.141
    r_dihedral_angle_3_deg 12.653
    r_dihedral_angle_4_deg 15.633
    r_chiral_restr 0.083
    r_gen_planes_refined 0.007
    r_gen_planes_other 0.001
    r_rigid_bond_restr 2.84
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3595
    Nucleic Acid Atoms 0
    Heterogen Atoms 25
    Solvent Atoms 691
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CLS
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution REFMAC 5.6.0117
    Structure Refinement REFMAC 5.6.0117
     
    Software
    data extraction pdb_extract version: 3.11
    refinement REFMAC5
    data reduction SCALEPACK
    data collection DENZO