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X-RAY DIFFRACTION
Materials and Methods page
3VUY
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion, hanging drop
    pH 8
    Temperature 293.0
    Details 10mM Tris-HCl, 150mM NaCl, 0.2M Na/K tartrate, 8% PEG 3350, pH 8.0, vapor diffusion, hanging drop, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 62.44 α = 90
    b = 62.44 β = 90
    c = 85.36 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 270
    Collection Date 2011-07-06
     
    Diffraction Radiation
    Monochromator Double-crystal monochromator
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type PHOTON FACTORY BEAMLINE BL-1A
    Wavelength List 1
    Site PHOTON FACTORY
    Beamline BL-1A
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.98
    Resolution(Low) 50
    Number Reflections(All) 25855
    Number Reflections(Observed) 25855
    Percent Possible(Observed) 99.8
    R Merge I(Observed) 0.096
    Redundancy 7.6
     
    High Resolution Shell Details
    Resolution(High) 1.98
    Resolution(Low) 2.01
    Percent Possible(All) 98.3
    R Merge I(Observed) 0.479
    Redundancy 4.4
    Number Unique Reflections(All) 1293
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.981
    Resolution(Low) 45.678
    Cut-off Sigma(F) 2.04
    Number of Reflections(all) 25820
    Number of Reflections(Observed) 25820
    Number of Reflections(R-Free) 1288
    Percent Reflections(Observed) 99.68
    R-Factor(Observed) 0.2184
    R-Work 0.2164
    R-Free 0.2549
    R-Free Selection Details random
     
    Temperature Factor Modeling
    Mean Isotropic B Value 42.3906
    Anisotropic B[1][1] 5.0841
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 5.0841
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -10.1682
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9809
    Shell Resolution(Low) 2.0602
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2711
    R-Factor(R-Work) 0.3738
    R-Factor(R-Free) 0.3938
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0602
    Shell Resolution(Low) 2.154
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2724
    R-Factor(R-Work) 0.3248
    R-Factor(R-Free) 0.3837
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.154
    Shell Resolution(Low) 2.2675
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2729
    R-Factor(R-Work) 0.2791
    R-Factor(R-Free) 0.3156
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2675
    Shell Resolution(Low) 2.4096
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2727
    R-Factor(R-Work) 0.2539
    R-Factor(R-Free) 0.2737
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4096
    Shell Resolution(Low) 2.5956
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2740
    R-Factor(R-Work) 0.2411
    R-Factor(R-Free) 0.2987
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5956
    Shell Resolution(Low) 2.8568
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2732
    R-Factor(R-Work) 0.2233
    R-Factor(R-Free) 0.2662
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8568
    Shell Resolution(Low) 3.2701
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2714
    R-Factor(R-Work) 0.1958
    R-Factor(R-Free) 0.2486
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2701
    Shell Resolution(Low) 4.1196
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2736
    R-Factor(R-Work) 0.1686
    R-Factor(R-Free) 0.1973
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1196
    Shell Resolution(Low) 45.6904
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2719
    R-Factor(R-Work) 0.1717
    R-Factor(R-Free) 0.2098
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 14.097
    f_plane_restr 0.002
    f_chiral_restr 0.046
    f_angle_d 0.627
    f_bond_d 0.012
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2541
    Nucleic Acid Atoms 0
    Heterogen Atoms 6
    Solvent Atoms 184
     
     
  •   Software and Computing Hide
    Computing
    Data Collection BSS
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution MOLREP
    Structure Refinement PHENIX (phenix.refine: 1.7.2_869)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction SCALEPACK