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An Information Portal to 105339 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
1YHS
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5.5
    Temperature 22.0
    Details ammonium phosphate, citrate buffer, NaCl, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 22K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 97.73 α = 90
    b = 97.73 β = 90
    c = 80.51 γ = 120
     
    Space Group
    Space Group Name:    P 65
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector IMAGE PLATE
    Type RIGAKU RAXIS IV
    Collection Date 2003-07-01
     
    Diffraction Radiation
    Monochromator Osmic mirror
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU RU200
    Wavelength List 1.54
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 2.0
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 2.15
    Resolution(Low) 19.58
    Number Reflections(All) 23830
    Number Reflections(Observed) 22615
    Percent Possible(Observed) 94.9
     
    High Resolution Shell Details
    Resolution(High) 2.15
    Resolution(Low) 2.23
    Percent Possible(All) 74.8
    Number Unique Reflections(All) 297
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.15
    Resolution(Low) 19.44
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 24232
    Number of Reflections(Observed) 22526
    Number of Reflections(R-Free) 1706
    Percent Reflections(Observed) 94.4
    R-Factor(All) 0.233
    R-Factor(Observed) 0.233
    R-Work 0.205
    R-Free 0.233
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 33.1
    Anisotropic B[1][1] 2.32
    Anisotropic B[1][2] 2.82
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 2.32
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -4.64
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.15
    Shell Resolution(Low) 2.28
    Number of Reflections(R-Free) 261
    Number of Reflections(R-Work) 2958
    R-Factor(R-Work) 0.266
    R-Factor(R-Free) 0.301
    R-Free Error 0.019
    Percent Reflections(Observed) 81.5
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_improper_angle_d 0.84
    c_dihedral_angle_d 23.1
    c_angle_deg 1.7
    c_bond_d 0.015
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2202
    Nucleic Acid Atoms 0
    Heterogen Atoms 35
    Solvent Atoms 151
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) R-AXIS
    Data Reduction (data scaling) D*TREK
    Structure Solution AMORE
    Structure Refinement CNS
     
    Software
    data extraction pdb_extract version: 1.501
    refinement CNS
    data processing D*trek version: 7.1SSI