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X-RAY DIFFRACTION
Materials and Methods page
4JKC
  •   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 = 76.19 α = 90
    b = 77.93 β = 90
    c = 93.68 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 2011-04-14
     
    Diffraction Radiation
    Monochromator Si
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source Synchrotron
    Type CLSI BEAMLINE 08ID-1
    Wavelength List 0.97949
    Site CLSI
    Beamline 08ID-1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 1.0
    Observed Criterion Sigma(I) 1.0
    Resolution(High) 1.5
    Resolution(Low) 50
    Number Reflections(Observed) 84356
    Percent Possible(Observed) 94.2
    R Merge I(Observed) 0.041
    Redundancy 4.5
     
    High Resolution Shell Details
    Resolution(High) 1.5
    Resolution(Low) 1.55
    Percent Possible(All) 67.1
    R Merge I(Observed) 0.37
    Redundancy 2.4
    Number Unique Reflections(All) 5931
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.5
    Resolution(Low) 35.29
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 84137
    Number of Reflections(R-Free) 4190
    Percent Reflections(Observed) 93.9
    R-Factor(Observed) 0.1299
    R-Work 0.1281
    R-Free 0.1636
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 24.3113
    Anisotropic B[1][1] -0.13
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.13
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.0
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5
    Shell Resolution(Low) 1.54
    Number of Reflections(R-Free) 208
    Number of Reflections(R-Work) 3804
    R-Factor(R-Work) 0.25
    R-Factor(R-Free) 0.264
    Percent Reflections(Observed) 62.38
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_sphericity_bonded 14.098
    r_sphericity_free 29.634
    r_bond_refined_d 0.01
    r_bond_other_d 0.001
    r_angle_refined_deg 1.356
    r_angle_other_deg 0.748
    r_dihedral_angle_1_deg 5.584
    r_dihedral_angle_2_deg 39.328
    r_dihedral_angle_3_deg 12.575
    r_dihedral_angle_4_deg 14.668
    r_chiral_restr 0.075
    r_gen_planes_refined 0.006
    r_gen_planes_other 0.001
    r_rigid_bond_restr 2.193
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3542
    Nucleic Acid Atoms 0
    Heterogen Atoms 18
    Solvent Atoms 636
     
     
  •   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