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X-RAY DIFFRACTION
Materials and Methods page
3NV1
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 8.5
    Temperature 293.0
    Details 20% PEG MME 2000, 0.1M Tris pH 8.5, 0.01M nickel chloride hexahydrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 70.58 α = 90
    b = 70.58 β = 90
    c = 50.14 γ = 120
     
    Space Group
    Space Group Name:    P 63
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 210r
    Collection Date 2010-05-14
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type PHOTON FACTORY BEAMLINE AR-NW12A
    Wavelength List 1.0
    Site PHOTON FACTORY
    Beamline AR-NW12A
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.5
    Resolution(Low) 50
    Number Reflections(Observed) 22811
    Percent Possible(Observed) 99.4
    R Merge I(Observed) 0.073
    B(Isotropic) From Wilson Plot 16.6
    Redundancy 4.6
     
    High Resolution Shell Details
    Resolution(High) 1.5
    Resolution(Low) 1.55
    Percent Possible(All) 99.5
    R Merge I(Observed) 0.397
    Mean I Over Sigma(Observed) 3.96
    Redundancy 4.5
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.5
    Resolution(Low) 26.1
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 21979
    Number of Reflections(Observed) 21979
    Number of Reflections(R-Free) 2184
    Percent Reflections(Observed) 96.0
    R-Factor(All) 0.184
    R-Factor(Observed) 0.181
    R-Work 0.181
    R-Free 0.205
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 17.4
    Anisotropic B[1][1] 0.72
    Anisotropic B[1][2] 1.21
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.72
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -1.44
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5
    Shell Resolution(Low) 1.59
    Number of Reflections(Observed) 3094
    Number of Reflections(R-Free) 347
    Number of Reflections(R-Work) 3094
    R-Factor(R-Work) 0.217
    R-Factor(R-Free) 0.259
    R-Free Error 0.014
    Percent Reflections(Observed) 90.9
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_improper_angle_d 0.88
    c_dihedral_angle_d 27.0
    c_angle_deg 1.5
    c_bond_d 0.005
     
    Coordinate Error
    Luzzati ESD(Observed) 0.15
    Luzzati Sigma A(Observed) 0.11
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.18
    Luzzati Sigma A(R-Free Set) 0.16
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1091
    Nucleic Acid Atoms 0
    Heterogen Atoms 1
    Solvent Atoms 180
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution Molrep
    Structure Refinement CNS 1.1
     
    Software
    refinement CNS version: 1.1
    model building Molrep
    data collection ADSC version: Quantum