POP-OUT | CLOSE

An Information Portal to 107049 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3UJP
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.5
    Temperature 290.0
    Details PEG 4000, sodium cacodylate, zinc chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 127.52 α = 90
    b = 127.52 β = 90
    c = 89.73 γ = 120
     
    Space Group
    Space Group Name:    P 31 2 1
     
     
  •   Diffraction Hide
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID23-1
    Wavelength List 0.934
    Site ESRF
    Beamline ID23-1
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.7
    Resolution(Low) 36.81
    Number Reflections(Observed) 21591
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.7
    Resolution(Low) 36.8
    Cut-off Sigma(F) 1.34
    Number of Reflections(Observed) 21591
    Number of Reflections(R-Free) 1089
    Percent Reflections(Observed) 91.99
    R-Factor(Observed) 0.2333
    R-Work 0.2307
    R-Free 0.2845
     
    Temperature Factor Modeling
    Anisotropic B[1][1] 1.2829
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 1.2829
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -2.5657
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7
    Shell Resolution(Low) 2.8229
    Number of Reflections(R-Free) 76
    Number of Reflections(R-Work) 1569
    R-Factor(R-Work) 0.354
    R-Factor(R-Free) 0.3533
    Percent Reflections(Observed) 57.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8229
    Shell Resolution(Low) 2.9717
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 2251
    R-Factor(R-Work) 0.3577
    R-Factor(R-Free) 0.3617
    Percent Reflections(Observed) 82.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9717
    Shell Resolution(Low) 3.1578
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2736
    R-Factor(R-Work) 0.3296
    R-Factor(R-Free) 0.3868
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1578
    Shell Resolution(Low) 3.4014
    Number of Reflections(R-Free) 164
    Number of Reflections(R-Work) 2751
    R-Factor(R-Work) 0.2945
    R-Factor(R-Free) 0.3563
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4014
    Shell Resolution(Low) 3.7434
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2770
    R-Factor(R-Work) 0.2475
    R-Factor(R-Free) 0.3287
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7434
    Shell Resolution(Low) 4.2844
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2757
    R-Factor(R-Work) 0.2217
    R-Factor(R-Free) 0.2652
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2844
    Shell Resolution(Low) 5.3951
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2811
    R-Factor(R-Work) 0.1867
    R-Factor(R-Free) 0.2415
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.3951
    Shell Resolution(Low) 36.8153
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2857
    R-Factor(R-Work) 0.2017
    R-Factor(R-Free) 0.2419
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.008
    f_chiral_restr 0.095
    f_dihedral_angle_d 19.287
    f_angle_d 1.733
    f_bond_d 0.026
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 6383
    Nucleic Acid Atoms 0
    Heterogen Atoms 29
    Solvent Atoms 12
     
     
  •   Software and Computing Hide
    Computing
    Data Collection DNA
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.6.1_357)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.6.1_357)
    model building PHASER
    data collection DNA