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X-RAY DIFFRACTION
Materials and Methods page
4DC8
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.5
    Temperature 293.0
    Details Protein Solution (20 mg/ml myoglobin, 60% saturated ammonium sulfate, 20 mM Tris, pH 7.5, 5 mM sodium azide, 1 mM EDTA); Well Solution (65% saturated ammonium sulfate, 20 mM Tris, pH 7.5, 1 mM EDTA); Cryoprotectant (68% ammonium sulfate, 20 mM Tris, pH 7.5, 5 mM EDTA, 20% glycerol), VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 35.36 α = 90
    b = 28.79 β = 106.05
    c = 63.06 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 300 mm CCD
    Details 20-micron minibeam collimator used
    Collection Date 2009-08-14
     
    Diffraction Radiation
    Monochromator Double Crystal Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 23-ID-B
    Wavelength List 1.0332
    Site APS
    Beamline 23-ID-B
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.5
    Resolution(Low) 50
    Number Reflections(All) 19833
    Number Reflections(Observed) 19833
    Percent Possible(Observed) 97.3
    R Merge I(Observed) 0.067
    B(Isotropic) From Wilson Plot 15.5
    Redundancy 4.7
     
    High Resolution Shell Details
    Resolution(High) 1.5
    Resolution(Low) 1.55
    Percent Possible(All) 90.1
    R Merge I(Observed) 0.299
    Mean I Over Sigma(Observed) 4.67
    R-Sym I(Observed) 0.299
    Redundancy 3.7
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 1.5
    Resolution(Low) 33.99
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 18718
    Number of Reflections(Observed) 18718
    Number of Reflections(R-Free) 907
    Percent Reflections(Observed) 94.2
    R-Factor(All) 0.185
    R-Factor(Observed) 0.183
    R-Work 0.183
    R-Free 0.218
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 16.1
    Anisotropic B[1][1] 2.67
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 1.0
    Anisotropic B[2][2] 2.25
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -4.92
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5
    Shell Resolution(Low) 1.59
    Number of Reflections(Observed) 2517
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2517
    R-Factor(R-Work) 0.231
    R-Factor(R-Free) 0.271
    R-Free Error 0.024
    Percent Reflections(Observed) 81.1
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_scangle_it 2.84
    c_scbond_it 1.97
    c_mcangle_it 1.34
    c_mcbond_it 0.92
    c_improper_angle_d 0.71
    c_dihedral_angle_d 16.6
    c_angle_deg 1.0
    c_bond_d 0.005
     
    Coordinate Error
    Luzzati ESD(Observed) 0.16
    Luzzati Sigma A(Observed) 0.1
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.2
    Luzzati Sigma A(R-Free Set) 0.11
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1195
    Nucleic Acid Atoms 0
    Heterogen Atoms 58
    Solvent Atoms 115
     
     
  •   Software and Computing Hide
    Computing
    Data Collection JBluice
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution CNS
    Structure Refinement CNS 1.3
     
    Software
    refinement CNS version: 1.3
    model building CNS
    data collection JBluice