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An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
1YYO
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.2
    Temperature 292.0
    Details Magnesium formate, PEG3350, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 292K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 84.49 α = 90
    b = 61.62 β = 90
    c = 131.11 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 BRUKER PROTEUM 300
    Details mirror
    Collection Date 2003-12-15
     
    Diffraction Radiation
    Monochromator Silicon
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 22-ID
    Wavelength List 1.000
    Site APS
    Beamline 22-ID
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.9
    Resolution(Low) 30
    Number Reflections(All) 14294
    Number Reflections(Observed) 14294
    Percent Possible(Observed) 90.8
    R Merge I(Observed) 0.06
    B(Isotropic) From Wilson Plot 61.9
    Redundancy 5.5
     
    High Resolution Shell Details
    Resolution(High) 2.9
    Resolution(Low) 3.0
    Percent Possible(All) 53.7
    R Merge I(Observed) 0.27
    Mean I Over Sigma(Observed) 1.7
    Redundancy 2.1
    Number Unique Reflections(All) 822
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 2.9
    Resolution(Low) 30.0
    Cut-off Sigma(I) 0.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 14294
    Number of Reflections(Observed) 14294
    Number of Reflections(R-Free) 847
    Percent Reflections(Observed) 90.8
    R-Factor(All) 0.225
    R-Factor(Observed) 0.225
    R-Work 0.223
    R-Free 0.292
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 70.7
    Anisotropic B[1][1] 3.22
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 3.76
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -6.98
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9
    Shell Resolution(Low) 3.08
    Number of Reflections(R-Free) 82
    Number of Reflections(R-Work) 1464
    R-Factor(R-Work) 0.344
    R-Factor(R-Free) 0.406
    R-Free Error 0.045
    Percent Reflections(Observed) 60.3
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_scangle_it 8.14
    c_scbond_it 5.67
    c_mcangle_it 5.66
    c_mcbond_it 3.61
    c_improper_angle_d 0.89
    c_bond_d 0.004
    c_angle_deg 0.9
    c_dihedral_angle_d 17.5
     
    Coordinate Error
    Luzzati ESD(Observed) 0.39
    Luzzati Sigma A(Observed) 0.36
    Luzzati Resolution Cutoff(Low) 30.0
    Luzzati ESD(R-Free Set) 0.54
    Luzzati Sigma A(R-Free Set) 0.35
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3666
    Nucleic Acid Atoms 1012
    Heterogen Atoms 8
    Solvent Atoms 35
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution CNS
    Structure Refinement CNS 1.0
     
    Software
    refinement CNS version: 1.0