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An Information Portal to 105906 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3ATY
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7
    Temperature 293.0
    Details PEG 1500, Ammonium fluoride, urea, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 56.29 α = 90
    b = 78.79 β = 93.37
    c = 78.8 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector IMAGE PLATE
    Type RIGAKU RAXIS V
    Collection Date 2006-07-04
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SPRING-8 BEAMLINE BL41XU
    Site SPRING-8
    Beamline BL41XU
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 1.7
    Resolution(Low) 50
    Number Reflections(Observed) 75469
    Percent Possible(Observed) 100.0
    B(Isotropic) From Wilson Plot 13.9
     
    High Resolution Shell Details
    Resolution(High) 1.7
    Resolution(Low) 1.76
    Percent Possible(All) 100.0
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.7
    Resolution(Low) 45.75
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 73953
    Number of Reflections(R-Free) 3755
    Percent Reflections(Observed) 97.8
    R-Factor(Observed) 0.17
    R-Work 0.17
    R-Free 0.195
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 15.9
    Anisotropic B[1][1] 1.19
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 1.2
    Anisotropic B[2][2] -1.26
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.08
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7
    Shell Resolution(Low) 1.81
    Number of Reflections(R-Free) 630
    Number of Reflections(R-Work) 11206
    R-Factor(R-Work) 0.184
    R-Factor(R-Free) 0.214
    R-Free Error 0.009
    Percent Reflections(Observed) 94.3
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_scangle_it 5.35
    c_scbond_it 3.98
    c_mcangle_it 3.14
    c_mcbond_it 2.51
    c_improper_angle_d 0.79
    c_bond_d 0.005
    c_angle_deg 1.3
    c_dihedral_angle_d 22.8
     
    Coordinate Error
    Luzzati ESD(Observed) 0.16
    Luzzati Sigma A(Observed) 0.05
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.19
    Luzzati Sigma A(R-Free Set) 0.1
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 5942
    Nucleic Acid Atoms 0
    Heterogen Atoms 62
    Solvent Atoms 719
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution AMoRE
    Structure Refinement CNS 1.1
     
    Software
    refinement CNS version: 1.1
    model building AMoRE
    data collection HKL-2000