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X-RAY DIFFRACTION
Materials and Methods page
3VYQ
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    Temperature 293.0
    Details 2mM zinc acetate, 100mM sodium cacodylate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 30.6 α = 75.28
    b = 34.09 β = 77.76
    c = 61.17 γ = 87.31
     
    Space Group
    Space Group Name:    P 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 95
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2007-06-28
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SPRING-8 BEAMLINE BL38B1
    Wavelength List 1.0
    Site SPRING-8
    Beamline BL38B1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 1.0
    Observed Criterion Sigma(I) 1.0
    Resolution(High) 2.5
    Resolution(Low) 50
    Number Reflections(All) 7786
    Number Reflections(Observed) 7225
    Percent Possible(Observed) 92.8
    R Merge I(Observed) 0.058
    B(Isotropic) From Wilson Plot 35.89
    Redundancy 2.9
     
    High Resolution Shell Details
    Resolution(High) 2.5
    Resolution(Low) 2.59
    Percent Possible(All) 67.4
    R Merge I(Observed) 0.125
    Mean I Over Sigma(Observed) 5.4
    Redundancy 1.7
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.525
    Resolution(Low) 32.972
    Cut-off Sigma(F) 0.07
    Number of Reflections(Observed) 7095
    Number of Reflections(R-Free) 323
    Percent Reflections(Observed) 90.27
    R-Factor(Observed) 0.1954
    R-Work 0.1934
    R-Free 0.2365
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 36.5379
    Anisotropic B[1][1] -4.2347
    Anisotropic B[1][2] -8.443
    Anisotropic B[1][3] -4.6272
    Anisotropic B[2][2] 5.9693
    Anisotropic B[2][3] 2.7744
    Anisotropic B[3][3] -1.7345
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5253
    Shell Resolution(Low) 3.1812
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 3093
    R-Factor(R-Work) 0.2485
    R-Factor(R-Free) 0.3347
    Percent Reflections(Observed) 82.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1812
    Shell Resolution(Low) 32.9752
    Number of Reflections(R-Free) 174
    Number of Reflections(R-Work) 3679
    R-Factor(R-Work) 0.1745
    R-Factor(R-Free) 0.2057
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.004
    f_chiral_restr 0.062
    f_dihedral_angle_d 23.241
    f_angle_d 1.161
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1030
    Nucleic Acid Atoms 429
    Heterogen Atoms 7
    Solvent Atoms 55
     
     
  •   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 PHENIX (phenix.refine: 1.6.4_486)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.6.4_486)
    model building Molrep
    data collection HKL-2000