POP-OUT | CLOSE
 
X-RAY DIFFRACTION
Materials and Methods page
4K32
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7
    Temperature 293.15
    Details 50 mM Na cacodylate, 1 mM spermine tetrahydrochloride, 1-20% 2-methyl-2,4-pentadiol (vs. 40% reservoir), 100-200 mM KCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 33.08 α = 90
    b = 90.76 β = 90
    c = 47.01 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315r
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID14-4
    Wavelength List 0.9394
    Site ESRF
    Beamline ID14-4
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 21.5
    Observed Criterion Sigma(I) 21.5
    Resolution(High) 2.5
    Resolution(Low) 50
    Number Reflections(All) 21134
    Number Reflections(Observed) 4294
    Percent Possible(Observed) 81.6
    R Merge I(Observed) 0.046
     
    High Resolution Shell Details
    Resolution(High) 2.5
    Resolution(Low) 2.57
    Percent Possible(All) 84.7
    R Merge I(Observed) 0.64
    Mean I Over Sigma(Observed) 2.0
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.5
    Resolution(Low) 23.505
    Cut-off Sigma(F) 2.04
    Number of Reflections(all) 4290
    Number of Reflections(Observed) 4290
    Number of Reflections(R-Free) 429
    Percent Reflections(Observed) 81.64
    R-Factor(Observed) 0.2096
    R-Work 0.2058
    R-Free 0.2445
     
    Temperature Factor Modeling
    Anisotropic B[1][1] 1.5826
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -7.1484
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 5.5658
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5004
    Shell Resolution(Low) 2.8616
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 1295
    R-Factor(R-Work) 0.3186
    R-Factor(R-Free) 0.3486
    Percent Reflections(Observed) 85.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8616
    Shell Resolution(Low) 3.6033
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 1300
    R-Factor(R-Work) 0.2102
    R-Factor(R-Free) 0.2987
    Percent Reflections(Observed) 83.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6033
    Shell Resolution(Low) 23.506
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 1266
    R-Factor(R-Work) 0.1768
    R-Factor(R-Free) 0.1956
    Percent Reflections(Observed) 77.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.008
    f_chiral_restr 0.057
    f_dihedral_angle_d 16.821
    f_angle_d 0.954
    f_bond_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 0
    Nucleic Acid Atoms 898
    Heterogen Atoms 68
    Solvent Atoms 11
     
     
  •   Software and Computing Hide
    Computing
    Data Collection DNA
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XDS
    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