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X-RAY DIFFRACTION
Materials and Methods page
4DBQ
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 8.5
    Temperature 277.0
    Details 50 mM Tris pH 8.5, 10% P8K, 1 mM TCEP, 6% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 73.31 α = 90
    b = 107.88 β = 90
    c = 179.95 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector AREA DETECTOR
    Type ADSC QUANTUM 315r
    Collection Date 2009-03-17
     
    Diffraction Radiation
    Monochromator Si III
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SOLEIL BEAMLINE PROXIMA 1
    Wavelength List 0.980100
    Site SOLEIL
    Beamline PROXIMA 1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) -3.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.6
    Resolution(Low) 19.98
    Number Reflections(All) 44722
    Number Reflections(Observed) 44526
    Percent Possible(Observed) 99.6
     
    High Resolution Shell Details
    Resolution(High) 2.6
    Resolution(Low) 2.7
    Percent Possible(All) 99.9
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.6
    Resolution(Low) 19.975
    Cut-off Sigma(F) 1.99
    Number of Reflections(all) 44722
    Number of Reflections(Observed) 44524
    Number of Reflections(R-Free) 2227
    Percent Reflections(Observed) 99.84
    R-Factor(Observed) 0.1723
    R-Work 0.1696
    R-Free 0.2235
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Data Not Available
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6
    Shell Resolution(Low) 2.6927
    Number of Reflections(R-Free) 220
    Number of Reflections(R-Work) 4170
    R-Factor(R-Work) 0.2571
    R-Factor(R-Free) 0.3256
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6927
    Shell Resolution(Low) 2.8003
    Number of Reflections(R-Free) 219
    Number of Reflections(R-Work) 4161
    R-Factor(R-Work) 0.2314
    R-Factor(R-Free) 0.2799
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8003
    Shell Resolution(Low) 2.9273
    Number of Reflections(R-Free) 220
    Number of Reflections(R-Work) 4181
    R-Factor(R-Work) 0.2256
    R-Factor(R-Free) 0.3121
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9273
    Shell Resolution(Low) 3.0811
    Number of Reflections(R-Free) 221
    Number of Reflections(R-Work) 4202
    R-Factor(R-Work) 0.2116
    R-Factor(R-Free) 0.2884
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0811
    Shell Resolution(Low) 3.2734
    Number of Reflections(R-Free) 220
    Number of Reflections(R-Work) 4187
    R-Factor(R-Work) 0.1881
    R-Factor(R-Free) 0.2379
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2734
    Shell Resolution(Low) 3.5249
    Number of Reflections(R-Free) 221
    Number of Reflections(R-Work) 4201
    R-Factor(R-Work) 0.1789
    R-Factor(R-Free) 0.2419
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5249
    Shell Resolution(Low) 3.8773
    Number of Reflections(R-Free) 223
    Number of Reflections(R-Work) 4222
    R-Factor(R-Work) 0.1678
    R-Factor(R-Free) 0.2208
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8773
    Shell Resolution(Low) 4.433
    Number of Reflections(R-Free) 222
    Number of Reflections(R-Work) 4225
    R-Factor(R-Work) 0.1365
    R-Factor(R-Free) 0.1727
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.433
    Shell Resolution(Low) 5.565
    Number of Reflections(R-Free) 227
    Number of Reflections(R-Work) 4315
    R-Factor(R-Work) 0.14
    R-Factor(R-Free) 0.1891
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.565
    Shell Resolution(Low) 19.975
    Number of Reflections(R-Free) 234
    Number of Reflections(R-Work) 4433
    R-Factor(R-Work) 0.1512
    R-Factor(R-Free) 0.2024
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.004
    f_chiral_restr 0.07
    f_dihedral_angle_d 15.476
    f_angle_d 1.095
    f_bond_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 7099
    Nucleic Acid Atoms 0
    Heterogen Atoms 51
    Solvent Atoms 392
     
     
  •   Software and Computing Hide
    Computing
    Data Collection DNA
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    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 DNA