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An Information Portal to 110790 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
1YPN
  •   Crystallization Hide
    Crystallization Experiments
    pH 5.3
    Details pH 5.3
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 88.47 α = 90
    b = 76.15 β = 90
    c = 50.79 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 293
     
    Diffraction Detector
    Detector CCD
    Collection Date 1995-11
     
    Diffraction Radiation
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID09
    Wavelength 0.4
    Site ESRF
    Beamline ID09
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.3
    Resolution(Low) 14.2
    Number Reflections(Observed) 11383
    Percent Possible(Observed) 72.9
    R Merge I(Observed) 0.113
    Redundancy 4.5
     
    High Resolution Shell Details
    Resolution(High) 2.3
    Resolution(Low) 2.36
    Percent Possible(All) 69.5
    R Merge I(Observed) 0.262
    Mean I Over Sigma(Observed) 2.3
    Redundancy 2.8
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.3
    Resolution(Low) 8.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 11383
    Number of Reflections(R-Free) 1176
    Percent Reflections(Observed) 72.9
    R-Factor(Observed) 0.199
    R-Work 0.199
    R-Free 0.29
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 22.0
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3
    Shell Resolution(Low) 2.4
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 1172
    R-Factor(R-Work) 0.277
    R-Factor(R-Free) 0.347
    Percent Reflections(Observed) 68.4
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    x_improper_angle_d 1.276
    x_bond_d 0.007
    x_angle_deg 1.671
    x_dihedral_angle_d 22.23
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2224
    Nucleic Acid Atoms 0
    Heterogen Atoms 30
    Solvent Atoms 103
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DARESBURY LAUE SUITE
    Data Reduction (data scaling) LAUENORM, CCP4 (AGROVATA)
    Structure Solution X-PLOR
    Structure Refinement X-PLOR 3.1
     
    Software
    refinement X-PLOR version: 3.1
    model building X-PLOR