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X-RAY DIFFRACTION
Materials and Methods page
3VPE
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5.8
    Temperature 293.0
    Details 28% PEG 2000, 0.1M sodium acetate, 0.2M ammonium sulfate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 67.83 α = 90
    b = 67.83 β = 90
    c = 48.67 γ = 120
     
    Space Group
    Space Group Name:    P 31
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 210r
    Collection Date 2010-10-16
     
    Diffraction Radiation
    Monochromator Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type PHOTON FACTORY BEAMLINE BL-5A
    Wavelength List 1.00000
    Site PHOTON FACTORY
    Beamline BL-5A
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.6
    Resolution(Low) 50
    Number Reflections(Observed) 32909
    Percent Possible(Observed) 99.4
    R Merge I(Observed) 0.051
    Redundancy 11.2
     
    High Resolution Shell Details
    Resolution(High) 1.6
    Resolution(Low) 1.63
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.216
    Redundancy 11.0
    Number Unique Reflections(All) 1654
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.6
    Resolution(Low) 27.83
    Number of Reflections(Observed) 31222
    Number of Reflections(R-Free) 1664
    Percent Reflections(Observed) 99.41
    R-Factor(Observed) 0.16644
    R-Work 0.16466
    R-Free 0.20021
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 21.118
    Anisotropic B[1][1] 0.0
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.0
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.0
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6
    Shell Resolution(Low) 1.641
    Number of Reflections(R-Free) 117
    Number of Reflections(R-Work) 2313
    R-Factor(R-Work) 0.21
    R-Factor(R-Free) 0.271
    Percent Reflections(Observed) 99.55
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_gen_planes_refined 0.007
    r_chiral_restr 0.095
    r_dihedral_angle_4_deg 19.447
    r_dihedral_angle_3_deg 12.543
    r_dihedral_angle_2_deg 31.467
    r_dihedral_angle_1_deg 6.076
    r_angle_refined_deg 1.431
    r_bond_refined_d 0.011
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1921
    Nucleic Acid Atoms 0
    Heterogen Atoms 53
    Solvent Atoms 277
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution AMoRE
    Structure Refinement REFMAC 5.6.0117
     
    Software
    refinement REFMAC version: 5.6.0117
    model building AMoRE
    data collection HKL-2000