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X-RAY DIFFRACTION
Materials and Methods page
3VSI
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.5
    Temperature 298.0
    Details 25% PEG 3350, 0.2M SODIUM CHLORIDE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 272.73 α = 90
    b = 48.26 β = 109.61
    c = 108.12 γ = 90
     
    Space Group
    Space Group Name:    C 1 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 95
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 210
    Collection Date 2007-06-16
     
    Diffraction Radiation
    Monochromator MIRRORS
    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) 2.5
    Resolution(Low) 69.34
    Number Reflections(All) 46662
    Number Reflections(Observed) 42370
    Percent Possible(Observed) 91.0
    R Merge I(Observed) 0.047
    B(Isotropic) From Wilson Plot 57.0
    Redundancy 3.2
     
    High Resolution Shell Details
    Resolution(High) 2.5
    Resolution(Low) 2.64
    Percent Possible(All) 81.6
    R Merge I(Observed) 0.336
    Mean I Over Sigma(Observed) 3.2
    R-Sym I(Observed) 0.336
    Redundancy 2.9
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.5
    Resolution(Low) 48.63
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 46662
    Number of Reflections(Observed) 40240
    Number of Reflections(R-Free) 2121
    Percent Reflections(Observed) 90.8
    R-Factor(All) 0.208
    R-Factor(Observed) 0.208
    R-Work 0.204
    R-Free 0.27
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model ISOTROPIC
    Mean Isotropic B Value 50.45
    Anisotropic B[1][1] 0.8
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -1.47
    Anisotropic B[2][2] -0.3
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -1.49
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5
    Shell Resolution(Low) 2.56
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2591
    R-Factor(R-Work) 0.28
    R-Factor(R-Free) 0.358
    Percent Reflections(Observed) 80.22
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_gen_planes_refined 0.011
    r_chiral_restr 0.072
    r_dihedral_angle_4_deg 13.681
    r_dihedral_angle_3_deg 17.688
    r_dihedral_angle_2_deg 37.586
    r_dihedral_angle_1_deg 5.18
    r_angle_refined_deg 1.089
    r_bond_refined_d 0.007
     
    Coordinate Error
    Luzzati ESD(Observed) 0.33
    Luzzati Sigma A(Observed) 0.36
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.44
    Luzzati Sigma A(R-Free Set) 0.44
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 8901
    Nucleic Acid Atoms 0
    Heterogen Atoms 24
    Solvent Atoms 271
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution PHASES
    Structure Refinement REFMAC 5.5.0102
     
    Software
    refinement REFMAC version: 5.5.0102
    model building PHASES
    data collection ADSC version: Quantum