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X-RAY DIFFRACTION
Materials and Methods page
3VUL
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 6.5
    Temperature 277.0
    Details 2.2M ammonium sulfate, 0.2M sodium chloride, 0.1M sodium cacodylate pH 6.5 , VAPOR DIFFUSION, SITTING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 161.78 α = 90
    b = 161.78 β = 90
    c = 87.72 γ = 120
     
    Space Group
    Space Group Name:    P 63 2 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 270
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type PHOTON FACTORY BEAMLINE AR-NE3A
    Site PHOTON FACTORY
    Beamline AR-NE3A
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 2.0
    Observed Criterion Sigma(I) 1.0
    Resolution(High) 2.8
    Resolution(Low) 50
    Number Reflections(Observed) 16976
    Percent Possible(Observed) 98.6
     
    High Resolution Shell Details
    Resolution(High) 2.8
    Resolution(Low) 2.9
    Percent Possible(All) 99.4
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.81
    Resolution(Low) 33.78
    Number of Reflections(Observed) 15954
    Number of Reflections(R-Free) 853
    Percent Reflections(Observed) 98.56
    R-Factor(Observed) 0.25207
    R-Work 0.24866
    R-Free 0.31501
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 51.439
    Anisotropic B[1][1] -0.02
    Anisotropic B[1][2] -0.01
    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) 2.805
    Shell Resolution(Low) 2.878
    Number of Reflections(R-Free) 64
    Number of Reflections(R-Work) 1124
    R-Factor(R-Work) 0.309
    R-Factor(R-Free) 0.325
    Percent Reflections(Observed) 97.22
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 3.857
    r_scbond_it 2.217
    r_mcangle_it 1.934
    r_mcbond_it 1.019
    r_gen_planes_refined 0.007
    r_chiral_restr 0.133
    r_dihedral_angle_4_deg 20.582
    r_dihedral_angle_3_deg 23.852
    r_dihedral_angle_2_deg 39.824
    r_dihedral_angle_1_deg 8.296
    r_angle_refined_deg 1.858
    r_bond_refined_d 0.018
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2859
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 37
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHASES
    Structure Refinement REFMAC 5.5.0072
     
    Software
    refinement REFMAC version: 5.5.0072
    model building PHASES
    data collection ADSC version: Quantum