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X-RAY DIFFRACTION
Materials and Methods page
3VND
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 7.5
    Temperature 277.0
    Details 2.0M Ammonium sulfate, 0.1M HEPES-NaOH (pH 7.5), 2% (w/v) PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 181.14 α = 90
    b = 182.78 β = 90
    c = 181.79 γ = 90
     
    Space Group
    Space Group Name:    C 2 2 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector IMAGE PLATE
    Type Bruker DIP-6040
    Collection Date 2009-10-20
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SPRING-8 BEAMLINE BL44XU
    Wavelength List 1.0
    Site SPRING-8
    Beamline BL44XU
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.6
    Resolution(Low) 50
    Number Reflections(Observed) 92082
    Percent Possible(Observed) 99.5
    R Merge I(Observed) 0.136
     
    High Resolution Shell Details
    Resolution(High) 2.6
    Resolution(Low) 2.64
    Percent Possible(All) 98.8
    R Merge I(Observed) 0.377
    Mean I Over Sigma(Observed) 2.22
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.6
    Resolution(Low) 48.79
    Number of Reflections(Observed) 87470
    Number of Reflections(R-Free) 4603
    Percent Reflections(Observed) 99.35
    R-Factor(Observed) 0.17472
    R-Work 0.17281
    R-Free 0.21094
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 31.832
    Anisotropic B[1][1] 0.69
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.74
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -1.43
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.599
    Shell Resolution(Low) 2.666
    Number of Reflections(R-Free) 303
    Number of Reflections(R-Work) 6306
    R-Factor(R-Work) 0.231
    R-Factor(R-Free) 0.291
    Percent Reflections(Observed) 97.18
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 5.696
    r_scbond_it 3.8
    r_mcangle_it 2.174
    r_mcbond_it 1.287
    r_gen_planes_other 0.001
    r_gen_planes_refined 0.009
    r_chiral_restr 0.134
    r_dihedral_angle_4_deg 23.762
    r_dihedral_angle_3_deg 23.214
    r_dihedral_angle_2_deg 42.358
    r_dihedral_angle_1_deg 8.318
    r_angle_other_deg 1.08
    r_angle_refined_deg 2.126
    r_bond_other_d 0.002
    r_bond_refined_d 0.019
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 15256
    Nucleic Acid Atoms 0
    Heterogen Atoms 190
    Solvent Atoms 1187
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution MOLREP
    Structure Refinement REFMAC 5.7.0029
     
    Software
    refinement REFMAC version: 5.5.0102
    model building MOLREP
    data collection HKL-2000