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An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
1YKR
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.5
    Temperature 298.0
    Details 20% PEG3000, 100mM Hepes, 200mM NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 53.25 α = 90
    b = 71.39 β = 90
    c = 71.42 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 200
     
    Diffraction Detector
    Detector CCD
    Type MARRESEARCH
    Collection Date 2001-09-01
     
    Diffraction Radiation
    Monochromator Yale Mirrors
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 19-ID
    Wavelength List 1.0
    Site APS
    Beamline 19-ID
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 1.0
    Observed Criterion Sigma(I) 1.0
    Resolution(High) 1.8
    Resolution(Low) 20
    Number Reflections(All) 25871
    Number Reflections(Observed) 25791
    Percent Possible(Observed) 99.7
    R Merge I(Observed) 0.047
    B(Isotropic) From Wilson Plot 15.0
    Redundancy 8.0
     
    High Resolution Shell Details
    Resolution(High) 1.8
    Resolution(Low) 1.86
    Percent Possible(All) 96.9
    R Merge I(Observed) 0.444
    Mean I Over Sigma(Observed) 4.0
    Redundancy 4.0
    Number Unique Reflections(All) 2468
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.8
    Resolution(Low) 20.0
    Cut-off Sigma(I) 1.0
    Cut-off Sigma(F) 1.0
    Number of Reflections(all) 25871
    Number of Reflections(Observed) 25791
    Number of Reflections(R-Free) 1244
    Percent Reflections(Observed) 99.7
    R-Factor(All) 0.275
    R-Factor(Observed) 0.26
    R-Work 0.255
    R-Free 0.271
    R-Free Selection Details Random
     
    Temperature Factor Modeling
    Isotropic Thermal Model Isotropic
    Anisotropic B[1][1] 2.163
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -8.406
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 6.243
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8
    Shell Resolution(Low) 1.83
    Number of Reflections(Observed) 972
    Number of Reflections(R-Free) 48
    R-Factor(R-Work) 0.37
    R-Factor(R-Free) 0.381
    R-Free Error 0.03
    Percent Reflections(Observed) 96.9
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_bond_d 0.013
    c_dihedral_angle_d 22.0
    c_mcangle_it 1.952
    c_mcbond_it 1.098
     
    Coordinate Error
    Luzzati ESD(Observed) 0.04
    Luzzati Sigma A(Observed) 0.2
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.045
    Luzzati Sigma A(R-Free Set) 0.32
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2398
    Nucleic Acid Atoms 0
    Heterogen Atoms 30
    Solvent Atoms 102
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) SCALEPACK
    Structure Solution AMORE
    Structure Refinement CNS
     
    Software
    refinement CNS
    model building AMoRE
    data reduction SCALEPACK
    data collection HKL-2000