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X-RAY DIFFRACTION
Materials and Methods page
4JPD
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 4.5
    Temperature 298.0
    Details 50% PEG400, 200mM LiSO4, 100mM Na acetate, 9.46mg/ml BuceA.18084.a.PW33863, direct cryoprotection, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 96.02 α = 90
    b = 96.02 β = 90
    c = 96.02 γ = 90
     
    Space Group
    Space Group Name:    P 43 3 2
     
     
  •   Diffraction Hide
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315r
    Collection Date 2012-10-18
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ALS BEAMLINE 5.0.1
    Wavelength List 0.97
    Site ALS
    Beamline 5.0.1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.9
    Resolution(Low) 42.98
    Number Reflections(Observed) 11700
    Percent Possible(Observed) 100.0
    R Merge I(Observed) 0.111
    B(Isotropic) From Wilson Plot 20.707
     
    High Resolution Shell Details
    Resolution(High) 1.9
    Resolution(Low) 2.0
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.437
    Mean I Over Sigma(Observed) 6.75
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.9
    Resolution(Low) 42.98
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 11700
    Number of Reflections(R-Free) 584
    Percent Reflections(Observed) 98.41
    R-Factor(Observed) 0.164
    R-Work 0.1624
    R-Free 0.1959
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 18.3399
    Anisotropic B[1][1] 0.0
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.0
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.0
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9
    Shell Resolution(Low) 1.949
    Number of Reflections(R-Free) 36
    Number of Reflections(R-Work) 805
    R-Factor(R-Work) 0.186
    R-Factor(R-Free) 0.228
    Percent Reflections(Observed) 93.65
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_mcangle_it 1.548
    r_mcbond_other 0.869
    r_bond_refined_d 0.011
    r_bond_other_d 0.001
    r_angle_refined_deg 1.349
    r_angle_other_deg 0.775
    r_dihedral_angle_1_deg 5.785
    r_dihedral_angle_2_deg 37.008
    r_dihedral_angle_3_deg 11.243
    r_dihedral_angle_4_deg 13.889
    r_chiral_restr 0.083
    r_gen_planes_refined 0.006
    r_gen_planes_other 0.001
    r_mcbond_it 0.895
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 832
    Nucleic Acid Atoms 0
    Heterogen Atoms 14
    Solvent Atoms 115
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution PHASER
    Structure Refinement REFMAC 5.7.0032
     
    Software
    data extraction pdb_extract version: 3.11
    refinement REFMAC5
    molecular replacement Phaser version: 2.5.2
    data reduction Xscale