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X-RAY DIFFRACTION
Materials and Methods page
1YPV
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 8.5
    Temperature 298.0
    Details PEG 4000, TRIS BUFFER, AMMONIUM SULFATE, 2-MERCAPTOETHANOL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 95.77 α = 90
    b = 95.77 β = 90
    c = 81.85 γ = 120
     
    Space Group
    Space Group Name:    P 31 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type SBC-1
    Details MONOCHROMATORS
    Collection Date 2003-06-03
     
    Diffraction Radiation
    Monochromator DOUBLE CRYSTALS (SI-111, SI-220)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 19-ID
    Wavelength 0.9793
    Wavelength List 0.9793
    Site APS
    Beamline 19-ID
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 1.8
    Resolution(Low) 50
    Number Reflections(Observed) 40526
    Percent Possible(Observed) 93.6
    R Merge I(Observed) 0.06
    B(Isotropic) From Wilson Plot 24.4
    Redundancy 4.8
     
    High Resolution Shell Details
    Resolution(High) 1.8
    Resolution(Low) 1.86
    Percent Possible(All) 91.2
    R Merge I(Observed) 0.563
    Redundancy 2.2
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.8
    Resolution(Low) 41.33
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 35328
    Number of Reflections(R-Free) 1772
    Percent Reflections(Observed) 87.1
    R-Factor(Observed) 0.2265
    R-Work 0.2265
    R-Free 0.2435
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 42.7
    Anisotropic B[1][1] -3.36
    Anisotropic B[1][2] -0.19
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -3.36
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 6.72
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8
    Shell Resolution(Low) 1.91
    Number of Reflections(Observed) 3639
    Number of Reflections(R-Free) 254
    Number of Reflections(R-Work) 4624
    R-Factor(R-Work) 0.359
    R-Factor(R-Free) 0.384
    R-Free Error 0.024
    Percent Reflections(Observed) 73.3
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_scangle_it 8.56
    c_scbond_it 7.77
    c_mcangle_it 2.87
    c_mcbond_it 2.25
    c_improper_angle_d 0.78
    c_dihedral_angle_d 23.6
    c_angle_deg 1.4
    c_bond_d 0.006
     
    Coordinate Error
    Luzzati ESD(Observed) 0.26
    Luzzati Sigma A(Observed) 0.3
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.29
    Luzzati Sigma A(R-Free Set) 0.33
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2102
    Nucleic Acid Atoms 0
    Heterogen Atoms 10
    Solvent Atoms 138
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) SCALEPACK
    Structure Solution CNS
    Structure Refinement CNS 1.1
     
    Software
    refinement CNS version: 1.1
    model building CNS
    data reduction SCALEPACK
    data collection D*TREK