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X-RAY DIFFRACTION
Materials and Methods page
4JCY
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    Temperature 289.0
    Details Protein was dialysed against the buffer containing 0.1 M NaCl, 50 mM TRIS-HCl pH 8.0, 1 mM EDTA. Crystallisation conditions: 0.2 M sodium iodide, 0.1 M Bis-Tris Propane pH 6.0, 15 % (w/v) PEG3350, 10 mM spermidine, protein dimer/DNA molar ratio 1:1, protein concentration 4.6 mg/ml , VAPOR DIFFUSION, HANGING DROP, temperature 289K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 62.34 α = 90
    b = 62.34 β = 90
    c = 158.08 γ = 120
     
    Space Group
    Space Group Name:    P 61
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 120
     
    Diffraction Detector
    Detector PIXEL
    Type PSI PILATUS 6M
    Collection Date 2012-06-05
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type DIAMOND BEAMLINE I02
    Wavelength List 0.9795
    Site DIAMOND
    Beamline I02
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 1.8
    Resolution(Low) 53.99
    Number Reflections(All) 32091
    Number Reflections(Observed) 30476
    Percent Possible(Observed) 99.5
    R Merge I(Observed) 0.059
    Redundancy 4.2
     
    High Resolution Shell Details
    Resolution(High) 1.8
    Resolution(Low) 1.9
    Percent Possible(All) 99.8
    R Merge I(Observed) 0.551
    Mean I Over Sigma(Observed) 2.6
    Redundancy 4.0
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.8
    Resolution(Low) 53.99
    Number of Reflections(all) 32091
    Number of Reflections(Observed) 30476
    Number of Reflections(R-Free) 1614
    Percent Reflections(Observed) 99.9
    R-Factor(Observed) 0.14788
    R-Work 0.14712
    R-Free 0.1626
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model Isotropic
    Mean Isotropic B Value 30.616
    Anisotropic B[1][1] 0.41
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.41
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.81
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8
    Shell Resolution(Low) 1.847
    Number of Reflections(R-Free) 109
    Number of Reflections(R-Work) 2270
    R-Factor(R-Work) 0.157
    R-Factor(R-Free) 0.192
    Percent Reflections(Observed) 99.83
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_gen_planes_refined 0.005
    r_chiral_restr 0.066
    r_dihedral_angle_4_deg 12.664
    r_dihedral_angle_3_deg 11.329
    r_dihedral_angle_2_deg 37.751
    r_dihedral_angle_1_deg 4.041
    r_angle_refined_deg 0.952
    r_bond_refined_d 0.004
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1494
    Nucleic Acid Atoms 855
    Heterogen Atoms 4
    Solvent Atoms 402
     
     
  •   Software and Computing Hide
    Computing
    Data Collection DNA
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALEPACK
    Structure Solution PHASER
    Structure Refinement REFMAC 5.7.0029
     
    Software
    refinement REFMAC version: 5.7.0029
    model building PHASER
    data collection DNA