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An Information Portal to 105025 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
1PY1
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.4
    Temperature 293.0
    Details PEG 3350, AMMONIUM SULFATE, CACODYLATE, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 70.14 α = 90
    b = 95.42 β = 90
    c = 107.97 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector IMAGE PLATE
    Type MARRESEARCH
    Collection Date 2003-03-17
     
    Diffraction Radiation
    Monochromator OSMIC OPTICS
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU RU300
    Wavelength List 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.6
    Resolution(Low) 40
    Number Reflections(All) 22869
    Number Reflections(Observed) 22025
    Percent Possible(Observed) 95.8
    R Merge I(Observed) 0.074
    B(Isotropic) From Wilson Plot 46.9
    Redundancy 6.9
     
    High Resolution Shell Details
    Resolution(High) 2.6
    Resolution(Low) 2.69
    Percent Possible(All) 98.9
    R Merge I(Observed) 0.373
    Mean I Over Sigma(Observed) 4.0
    Number Unique Reflections(All) 2229
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.6
    Resolution(Low) 39.45
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 22869
    Number of Reflections(Observed) 22006
    Number of Reflections(R-Free) 858
    Percent Reflections(Observed) 95.8
    R-Factor(All) 0.24
    R-Factor(Observed) 0.236
    R-Work 0.236
    R-Free 0.288
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 52.5
    Anisotropic B[1][1] 4.5
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 15.37
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -19.87
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6
    Shell Resolution(Low) 2.69
    Number of Reflections(R-Free) 67
    Number of Reflections(R-Work) 1883
    R-Factor(R-Work) 0.392
    R-Factor(R-Free) 0.511
    R-Free Error 0.062
    Percent Reflections(Observed) 86.5
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_scangle_it 3.32
    c_scbond_it 2.09
    c_mcangle_it 2.73
    c_mcbond_it 1.56
    c_improper_angle_d 0.98
    c_dihedral_angle_d 19.4
    c_angle_deg 1.2
    c_bond_d 0.011
     
    Coordinate Error
    Luzzati ESD(R-Free Set) 0.51
    Luzzati Sigma A(R-Free Set) 0.53
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4739
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 37
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution AMORE
    Structure Refinement CNS 1.1
     
    Software
    refinement CNS version: 1.1