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An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3VT5
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7
    Temperature 293.0
    Details MOPS-Na, sodium formate, PEG 4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 153.17 α = 90
    b = 42.56 β = 96.1
    c = 42.18 γ = 90
     
    Space Group
    Space Group Name:    C 1 2 1
     
     
  •   Diffraction Hide
    Diffraction Detector
    Collection Date 2007-10-25
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type PHOTON FACTORY BEAMLINE BL-6A
    Wavelength List 0.97800
    Site PHOTON FACTORY
    Beamline BL-6A
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.11
    Resolution(Low) 50
    Number Reflections(Observed) 14420
    B(Isotropic) From Wilson Plot 25.2
     
    High Resolution Shell Details
    Resolution(High) 2.11
    Resolution(Low) 2.18
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.11
    Resolution(Low) 41.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 14420
    Number of Reflections(R-Free) 1453
    Percent Reflections(Observed) 90.9
    R-Factor(Observed) 0.224
    R-Work 0.224
    R-Free 0.266
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 53.0
    Anisotropic B[1][1] -14.46
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -9.17
    Anisotropic B[2][2] 23.86
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -9.39
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1
    Shell Resolution(Low) 2.23
    Number of Reflections(R-Free) 182
    Number of Reflections(R-Work) 1801
    R-Factor(R-Work) 0.356
    R-Factor(R-Free) 0.367
    R-Free Error 0.027
    Percent Reflections(Observed) 74.9
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_scangle_it 6.11
    c_scbond_it 4.82
    c_mcangle_it 2.48
    c_mcbond_it 1.51
    c_improper_angle_d 0.69
    c_bond_d 0.005
    c_angle_deg 0.7
    c_dihedral_angle_d 19.2
     
    Coordinate Error
    Luzzati ESD(Observed) 0.29
    Luzzati Sigma A(Observed) 0.4
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.36
    Luzzati Sigma A(R-Free Set) 0.41
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2012
    Nucleic Acid Atoms 0
    Heterogen Atoms 33
    Solvent Atoms 24
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution CNS
    Structure Refinement CNS 1.1
     
    Software
    refinement CNS version: 1.1
    model building CNS
    data collection HKL-2000