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An Information Portal to 105339 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4DY1
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 8.5
    Temperature 291.0
    Details TRIS 0.1M, DMSO 10%, PEG8000 7%, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 90.83 α = 90
    b = 64.6 β = 96.39
    c = 71.09 γ = 90
     
    Space Group
    Space Group Name:    C 1 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 225 mm CCD
    Details MIRROR
    Collection Date 2011-07-12
     
    Diffraction Radiation
    Monochromator DOUBLE CRYSTAL MONOCHROMATOR
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type BESSY BEAMLINE 14.2
    Wavelength List 0.91841
    Site BESSY
    Beamline 14.2
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.05
    Resolution(Low) 50
    Number Reflections(All) 25405
    Number Reflections(Observed) 25405
    Percent Possible(Observed) 97.9
    B(Isotropic) From Wilson Plot 17.6
    Redundancy 3.6
     
    High Resolution Shell Details
    Resolution(High) 2.045
    Resolution(Low) 2.09
    Percent Possible(All) 84.4
    R-Sym I(Observed) 0.375
    Redundancy 2.3
    Number Unique Reflections(All) 1085
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.045
    Resolution(Low) 25.158
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 23698
    Number of Reflections(Observed) 23698
    Number of Reflections(R-Free) 1203
    Percent Reflections(Observed) 91.16
    R-Factor(Observed) 0.1683
    R-Work 0.1655
    R-Free 0.22
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model isotropic
    Mean Isotropic B Value 16.72
    Anisotropic B[1][1] 3.6715
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -0.861
    Anisotropic B[2][2] -2.4108
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -1.2607
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.045
    Shell Resolution(Low) 2.1264
    Number of Reflections(R-Free) 116
    Number of Reflections(R-Work) 2002
    R-Factor(R-Work) 0.2009
    R-Factor(R-Free) 0.271
    Percent Reflections(Observed) 74.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1264
    Shell Resolution(Low) 2.2231
    Number of Reflections(R-Free) 122
    Number of Reflections(R-Work) 2327
    R-Factor(R-Work) 0.202
    R-Factor(R-Free) 0.297
    Percent Reflections(Observed) 84.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2231
    Shell Resolution(Low) 2.3402
    Number of Reflections(R-Free) 114
    Number of Reflections(R-Work) 2173
    R-Factor(R-Work) 0.243
    R-Factor(R-Free) 0.3099
    Percent Reflections(Observed) 80.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3402
    Shell Resolution(Low) 2.4867
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2503
    R-Factor(R-Work) 0.1738
    R-Factor(R-Free) 0.2595
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4867
    Shell Resolution(Low) 2.6785
    Number of Reflections(R-Free) 121
    Number of Reflections(R-Work) 2656
    R-Factor(R-Work) 0.1733
    R-Factor(R-Free) 0.2319
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6785
    Shell Resolution(Low) 2.9477
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2643
    R-Factor(R-Work) 0.157
    R-Factor(R-Free) 0.2475
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9477
    Shell Resolution(Low) 3.3734
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2696
    R-Factor(R-Work) 0.1538
    R-Factor(R-Free) 0.1979
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3734
    Shell Resolution(Low) 4.2468
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2718
    R-Factor(R-Work) 0.1339
    R-Factor(R-Free) 0.1796
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2468
    Shell Resolution(Low) 25.1597
    Number of Reflections(R-Free) 167
    Number of Reflections(R-Work) 2777
    R-Factor(R-Work) 0.1571
    R-Factor(R-Free) 0.1836
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.005
    f_chiral_restr 0.066
    f_dihedral_angle_d 13.691
    f_angle_d 1.053
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2858
    Nucleic Acid Atoms 0
    Heterogen Atoms 3
    Solvent Atoms 362
     
     
  •   Software and Computing Hide
    Computing
    Data Collection MAR345dtb
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.7_650)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7_650)
    model building PHASER
    data collection MAR345dtb