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An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3VLJ
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6
    Temperature 288.0
    Details 1mM o-Dianisidine, 2.36-2.58M Ammonium sulfate, 0.5M potassium chloride, 20mM sodium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 288K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 315.21 α = 90
    b = 80.76 β = 99.5
    c = 75.43 γ = 90
     
    Space Group
    Space Group Name:    C 1 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 210
    Collection Date 2006-06-16
     
    Diffraction Radiation
    Monochromator SAGITALLY FOCUSED Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type PHOTON FACTORY BEAMLINE AR-NW12A
    Wavelength List 1
    Site PHOTON FACTORY
    Beamline AR-NW12A
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 1.0
    Observed Criterion Sigma(I) 1.0
    Resolution(High) 1.7
    Resolution(Low) 50
    Number Reflections(All) 203754
    Number Reflections(Observed) 203754
    Percent Possible(Observed) 100.0
    R Merge I(Observed) 0.133
    B(Isotropic) From Wilson Plot 20.0
    Redundancy 7.5
     
    High Resolution Shell Details
    Resolution(High) 1.7
    Resolution(Low) 1.78
    Percent Possible(All) 99.9
    R Merge I(Observed) 0.643
    Mean I Over Sigma(Observed) 3.2
    Redundancy 3.2
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.7
    Resolution(Low) 36.74
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 203754
    Number of Reflections(R-Free) 10041
    Percent Reflections(Observed) 99.5
    R-Work 0.216
    R-Free 0.234
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 24.8222
    Anisotropic B[1][1] -5.39
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -3.03
    Anisotropic B[2][2] 0.07
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 5.31
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7
    Shell Resolution(Low) 1.81
    Number of Reflections(R-Free) 1612
    Number of Reflections(R-Work) 31181
    R-Factor(R-Work) 0.254
    R-Factor(R-Free) 0.27
    R-Free Error 0.007
    Percent Reflections(Observed) 96.4
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_improper_angle_d 0.87
    c_dihedral_angle_d 21.7
    c_angle_deg 1.4
    c_bond_d 0.006
     
    Coordinate Error
    Luzzati ESD(Observed) 0.21
    Luzzati Sigma A(Observed) 0.12
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.23
    Luzzati Sigma A(R-Free Set) 0.13
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 11121
    Nucleic Acid Atoms 0
    Heterogen Atoms 126
    Solvent Atoms 747
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    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 ADSC version: Quantum