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X-RAY DIFFRACTION
Materials and Methods page
4GQL
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 8.5
    Temperature 293.0
    Details Reservoir: 25% PEG 10000, 0.2M imidazole malate. Cryoprotectant: 27% PEG 8000, 15% MPEG 550, 10% glycerol, .01M hydroxamic acid, 90mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 69.58 α = 90
    b = 63.39 β = 90
    c = 36.9 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
    Details bent cylindrical mirror
    Collection Date 2009-02-23
     
    Diffraction Radiation
    Monochromator horizontally diffracting Si (111) monochromator and Pt coated mirrors in Kirkpatrick-Baez geometry for focusing
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID23-1
    Wavelength List 0.979300
    Site ESRF
    Beamline ID23-1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.15
    Resolution(Low) 50
    Number Reflections(All) 58830
    Number Reflections(Observed) 58014
    Percent Possible(Observed) 98.6
    R Merge I(Observed) 0.091
    B(Isotropic) From Wilson Plot 13.934
    Redundancy 6.9
     
    High Resolution Shell Details
    Resolution(High) 1.15
    Resolution(Low) 1.22
    Percent Possible(All) 96.5
    R Merge I(Observed) 1.3
    Mean I Over Sigma(Observed) 2.3
    R-Sym I(Observed) 1.2
    Redundancy 6.73
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.15
    Resolution(Low) 32.599
    Cut-off Sigma(F) 1.99
    Number of Reflections(all) 58014
    Number of Reflections(Observed) 57994
    Number of Reflections(R-Free) 2900
    Percent Reflections(Observed) 98.69
    R-Factor(Observed) 0.1343
    R-Work 0.1333
    R-Free 0.1545
     
    Temperature Factor Modeling
    Isotropic Thermal Model Anisotropic
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.15
    Shell Resolution(Low) 1.1689
    Number of Reflections(R-Free) 124
    Number of Reflections(R-Work) 2342
    R-Factor(R-Work) 0.312
    R-Factor(R-Free) 0.3186
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.1689
    Shell Resolution(Low) 1.189
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2641
    R-Factor(R-Work) 0.252
    R-Factor(R-Free) 0.232
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.189
    Shell Resolution(Low) 1.2107
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2613
    R-Factor(R-Work) 0.2202
    R-Factor(R-Free) 0.2341
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.2107
    Shell Resolution(Low) 1.234
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2638
    R-Factor(R-Work) 0.2176
    R-Factor(R-Free) 0.2582
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.234
    Shell Resolution(Low) 1.2591
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2593
    R-Factor(R-Work) 0.1946
    R-Factor(R-Free) 0.2375
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.2591
    Shell Resolution(Low) 1.2865
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2649
    R-Factor(R-Work) 0.1761
    R-Factor(R-Free) 0.2652
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.2865
    Shell Resolution(Low) 1.3164
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2631
    R-Factor(R-Work) 0.1642
    R-Factor(R-Free) 0.1911
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3164
    Shell Resolution(Low) 1.3494
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2606
    R-Factor(R-Work) 0.1386
    R-Factor(R-Free) 0.1624
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3494
    Shell Resolution(Low) 1.3859
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2638
    R-Factor(R-Work) 0.1261
    R-Factor(R-Free) 0.1409
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3859
    Shell Resolution(Low) 1.4266
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2648
    R-Factor(R-Work) 0.1182
    R-Factor(R-Free) 0.1495
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4266
    Shell Resolution(Low) 1.4727
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2628
    R-Factor(R-Work) 0.1081
    R-Factor(R-Free) 0.1307
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4727
    Shell Resolution(Low) 1.5253
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2634
    R-Factor(R-Work) 0.1065
    R-Factor(R-Free) 0.1338
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5253
    Shell Resolution(Low) 1.5864
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2649
    R-Factor(R-Work) 0.0982
    R-Factor(R-Free) 0.126
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5864
    Shell Resolution(Low) 1.6586
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2654
    R-Factor(R-Work) 0.1016
    R-Factor(R-Free) 0.1416
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6586
    Shell Resolution(Low) 1.746
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2664
    R-Factor(R-Work) 0.1061
    R-Factor(R-Free) 0.1249
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.746
    Shell Resolution(Low) 1.8554
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2636
    R-Factor(R-Work) 0.1091
    R-Factor(R-Free) 0.1279
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8554
    Shell Resolution(Low) 1.9986
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2670
    R-Factor(R-Work) 0.1108
    R-Factor(R-Free) 0.1214
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9986
    Shell Resolution(Low) 2.1997
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2695
    R-Factor(R-Work) 0.1119
    R-Factor(R-Free) 0.1236
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1997
    Shell Resolution(Low) 2.5179
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2684
    R-Factor(R-Work) 0.1189
    R-Factor(R-Free) 0.1331
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5179
    Shell Resolution(Low) 3.1719
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2732
    R-Factor(R-Work) 0.1276
    R-Factor(R-Free) 0.1492
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1719
    Shell Resolution(Low) 32.6125
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 2449
    R-Factor(R-Work) 0.1504
    R-Factor(R-Free) 0.1702
    Percent Reflections(Observed) 85.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.007
    f_chiral_restr 0.112
    f_dihedral_angle_d 15.377
    f_angle_d 1.5
    f_bond_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1246
    Nucleic Acid Atoms 0
    Heterogen Atoms 57
    Solvent Atoms 303
     
     
  •   Software and Computing Hide
    Computing
    Data Collection DNA
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XDS
    Structure Solution MOLREP
    Structure Refinement PHENIX (phenix.refine: 1.8_1069)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.8_1069)
    model building MOLREP
    data collection DNA