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X-RAY DIFFRACTION
Materials and Methods page
4HZN
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.75
    Temperature 298.0
    Details Protein solution: 45 mg/mL protein in 10 mM NaCl and 10 mM Tris-HCl, 2.5 mM methylmalonyl-CoA, pH 8.0. Precipitant solution: 12 - 18% glycerol, 1.3 - 1.6 M (NH4)2SO4, 0.1 M Tris-HCl, pH 7.0 - 8.5 (1:1, protein:well), VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 60.17 α = 90
    b = 60.17 β = 90
    c = 311.19 γ = 120
     
    Space Group
    Space Group Name:    P 61 2 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 300 mm CCD
    Collection Date 2009-06-08
     
    Diffraction Radiation
    Monochromator Si(111)
    Diffraction Protocol MAD
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 21-ID-D
    Wavelength List 0.97941, 1.127
    Site APS
    Beamline 21-ID-D
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.25
    Resolution(Low) 28.06
    Number Reflections(All) 17112
    Number Reflections(Observed) 16907
    Percent Possible(Observed) 98.8
    R Merge I(Observed) 0.074
    Redundancy 17.3
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MAD
    reflnsShellList 2.25
    Resolution(Low) 28.06
    Number of Reflections(all) 16907
    Number of Reflections(Observed) 15889
    Number of Reflections(R-Free) 869
    Percent Reflections(Observed) 100.0
    R-Factor(Observed) 0.20245
    R-Work 0.19977
    R-Free 0.25381
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 23.1
    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) 2.25
    Shell Resolution(Low) 2.308
    Number of Reflections(R-Free) 67
    Number of Reflections(R-Work) 1147
    R-Factor(R-Work) 0.196
    R-Factor(R-Free) 0.266
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 2.606
    r_scbond_it 1.625
    r_mcangle_it 1.098
    r_mcbond_it 0.573
    r_gen_planes_refined 0.005
    r_chiral_restr 0.082
    r_dihedral_angle_4_deg 16.91
    r_dihedral_angle_3_deg 14.211
    r_dihedral_angle_2_deg 34.695
    r_dihedral_angle_1_deg 6.077
    r_angle_refined_deg 1.233
    r_bond_refined_d 0.009
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2340
    Nucleic Acid Atoms 0
    Heterogen Atoms 39
    Solvent Atoms 113
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) SCALEPACK
    Structure Solution SOLVE
    Structure Refinement REFMAC 5.5.0109
     
    Software
    refinement REFMAC version: 5.5.0109
    model building SOLVE
    data collection HKL-2000