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X-RAY DIFFRACTION
Materials and Methods page
4HBJ
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 7.5
    Temperature 298.0
    Details drop: 14 mg/mL protein, 0.8 M Potassium Phosphate, 5 mM Tris, 5 uM EDTA, 3.6% 1,2,3-heptanetriol, 2.0% dioxane, 140 mM sodium chloride, 0.045% LDAO, reservoir: 1.6 M potassium phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 139.54 α = 90
    b = 139.54 β = 90
    c = 185.07 γ = 120
     
    Space Group
    Space Group Name:    P 31 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 225 mm CCD
    Collection Date 2012-02-04
     
    Diffraction Radiation
    Monochromator diamond(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 21-ID-F
    Wavelength 1.00000
    Site APS
    Beamline 21-ID-F
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.74
    Resolution(Low) 19.87
    Number Reflections(Observed) 54952
    Percent Possible(Observed) 99.4
    R Merge I(Observed) 0.123
    B(Isotropic) From Wilson Plot 55.11
     
    High Resolution Shell Details
    Resolution(High) 2.74
    Resolution(Low) 2.81
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.758
    Mean I Over Sigma(Observed) 2.7
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.74
    Resolution(Low) 19.867
    Number of Reflections(Observed) 54952
    Number of Reflections(R-Free) 2748
    Percent Reflections(Observed) 99.7
    R-Factor(Observed) 0.191
    R-Work 0.189
    R-Free 0.223
     
    Temperature Factor Modeling
    Mean Isotropic B Value 44.85
    Anisotropic B[1][1] 0.01
    Anisotropic B[1][2] 0.01
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.01
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.02
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.74
    Shell Resolution(Low) 2.81
    Number of Reflections(R-Free) 198
    Number of Reflections(R-Work) 3762
    R-Factor(R-Work) 0.265
    R-Factor(R-Free) 0.341
    Percent Reflections(Observed) 99.97
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 3.976
    r_scbond_it 2.555
    r_mcangle_it 1.678
    r_mcbond_it 0.885
    r_gen_planes_refined 0.01
    r_chiral_restr 0.142
    r_dihedral_angle_4_deg 22.442
    r_dihedral_angle_3_deg 20.163
    r_dihedral_angle_2_deg 34.535
    r_dihedral_angle_1_deg 7.113
    r_angle_refined_deg 2.38
    r_bond_refined_d 0.022
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 6419
    Nucleic Acid Atoms 0
    Heterogen Atoms 498
    Solvent Atoms 65
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution Refmac5
    Structure Refinement REFMAC 5.5.0109
     
    Software
    data extraction pdb_extract version: 3.11
    refinement REFMAC5 version: 5.5.0109
    data reduction Xscale