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X-RAY DIFFRACTION
Materials and Methods page
3VNH
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7
    Temperature 277.0
    Details 0.2M HEPES (pH 7.0), 10mM Magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 85.37 α = 90
    b = 85.37 β = 90
    c = 145.9 γ = 120
     
    Space Group
    Space Group Name:    P 65 2 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type RIGAKU JUPITER 210
    Collection Date 2010-02-02
     
    Diffraction Radiation
    Monochromator bending magnet
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SPRING-8 BEAMLINE BL26B2
    Wavelength List 1.000
    Site SPRING-8
    Beamline BL26B2
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) -3.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.1
    Resolution(Low) 500
    Number Reflections(Observed) 19041
    Percent Possible(Observed) 76.3
    R Merge I(Observed) 0.095
    B(Isotropic) From Wilson Plot 11.9
    Redundancy 32.1
     
    High Resolution Shell Details
    Resolution(High) 2.1
    Resolution(Low) 2.18
    Percent Possible(All) 76.3
    R Merge I(Observed) 0.371
    Mean I Over Sigma(Observed) 10.27
    R-Sym I(Observed) 0.33
    Redundancy 32.3
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.1
    Resolution(Low) 36.84
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 19041
    Number of Reflections(Observed) 18954
    Number of Reflections(R-Free) 960
    Percent Reflections(Observed) 99.6
    R-Factor(Observed) 0.201
    R-Work 0.201
    R-Free 0.211
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 22.2
    Anisotropic B[1][1] 0.02
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.02
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.03
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1
    Shell Resolution(Low) 2.23
    Number of Reflections(R-Free) 165
    Number of Reflections(R-Work) 2896
    R-Factor(R-Work) 0.236
    R-Factor(R-Free) 0.247
    R-Free Error 0.019
    Percent Reflections(Observed) 99.2
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_scangle_it 2.9
    c_scbond_it 1.99
    c_mcangle_it 1.59
    c_mcbond_it 1.03
    c_improper_angle_d 0.92
    c_bond_d 0.012
    c_angle_deg 1.7
    c_dihedral_angle_d 27.9
     
    Coordinate Error
    Luzzati ESD(Observed) 0.23
    Luzzati Sigma A(Observed) 0.18
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.25
    Luzzati Sigma A(R-Free Set) 0.19
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2217
    Nucleic Acid Atoms 0
    Heterogen Atoms 26
    Solvent Atoms 247
     
     
  •   Software and Computing Hide
    Computing
    Data Collection BSS
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution MOLREP
    Structure Refinement CNS 1.3
     
    Software
    refinement CNS version: 1.3
    model building MOLREP
    data collection BSS