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X-RAY DIFFRACTION
Materials and Methods page
4E3T
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.5
    Temperature 298.15
    Details 50mM MES, 2% PEG8000, 30% MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 85.77 α = 90
    b = 85.97 β = 90
    c = 88.73 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
    Collection Date 2010-11-20
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID14-4
    Wavelength List 0.9393
    Site ESRF
    Beamline ID14-4
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.65
    Resolution(Low) 30
    Number Reflections(Observed) 79417
    Percent Possible(Observed) 99.9
    B(Isotropic) From Wilson Plot 18.42
     
    High Resolution Shell Details
    Resolution(High) 1.65
    Resolution(Low) 1.74
    Percent Possible(All) 99.5
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.65
    Resolution(Low) 29.576
    Cut-off Sigma(F) 1.33
    Number of Reflections(Observed) 75264
    Number of Reflections(R-Free) 3988
    Percent Reflections(Observed) 99.78
    R-Factor(Observed) 0.1749
    R-Work 0.1733
    R-Free 0.2055
    R-Free Selection Details 5
     
    Temperature Factor Modeling
    Mean Isotropic B Value 26.5965
    Anisotropic B[1][1] -1.669
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 6.7365
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -5.0675
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.65
    Shell Resolution(Low) 1.6701
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2633
    R-Factor(R-Work) 0.2824
    R-Factor(R-Free) 0.3276
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6701
    Shell Resolution(Low) 1.6913
    Number of Reflections(R-Free) 124
    Number of Reflections(R-Work) 2673
    R-Factor(R-Work) 0.2648
    R-Factor(R-Free) 0.2679
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6913
    Shell Resolution(Low) 1.7135
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2651
    R-Factor(R-Work) 0.2495
    R-Factor(R-Free) 0.2804
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7135
    Shell Resolution(Low) 1.737
    Number of Reflections(R-Free) 161
    Number of Reflections(R-Work) 2616
    R-Factor(R-Work) 0.2428
    R-Factor(R-Free) 0.3003
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.737
    Shell Resolution(Low) 1.7618
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2703
    R-Factor(R-Work) 0.2283
    R-Factor(R-Free) 0.2769
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7618
    Shell Resolution(Low) 1.7881
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2644
    R-Factor(R-Work) 0.2189
    R-Factor(R-Free) 0.2383
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7881
    Shell Resolution(Low) 1.816
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2656
    R-Factor(R-Work) 0.2111
    R-Factor(R-Free) 0.2386
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.816
    Shell Resolution(Low) 1.8458
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2650
    R-Factor(R-Work) 0.2063
    R-Factor(R-Free) 0.2551
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8458
    Shell Resolution(Low) 1.8776
    Number of Reflections(R-Free) 123
    Number of Reflections(R-Work) 2695
    R-Factor(R-Work) 0.1871
    R-Factor(R-Free) 0.2485
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8776
    Shell Resolution(Low) 1.9118
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2663
    R-Factor(R-Work) 0.1862
    R-Factor(R-Free) 0.2231
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9118
    Shell Resolution(Low) 1.9485
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2674
    R-Factor(R-Work) 0.1782
    R-Factor(R-Free) 0.2243
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9485
    Shell Resolution(Low) 1.9883
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2684
    R-Factor(R-Work) 0.1951
    R-Factor(R-Free) 0.2148
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9883
    Shell Resolution(Low) 2.0315
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2665
    R-Factor(R-Work) 0.1801
    R-Factor(R-Free) 0.2414
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0315
    Shell Resolution(Low) 2.0788
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2641
    R-Factor(R-Work) 0.1803
    R-Factor(R-Free) 0.2078
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0788
    Shell Resolution(Low) 2.1307
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2702
    R-Factor(R-Work) 0.1806
    R-Factor(R-Free) 0.2231
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1307
    Shell Resolution(Low) 2.1883
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2659
    R-Factor(R-Work) 0.1804
    R-Factor(R-Free) 0.2022
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1883
    Shell Resolution(Low) 2.2527
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2699
    R-Factor(R-Work) 0.1681
    R-Factor(R-Free) 0.2241
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2527
    Shell Resolution(Low) 2.3254
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2674
    R-Factor(R-Work) 0.171
    R-Factor(R-Free) 0.2072
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3254
    Shell Resolution(Low) 2.4084
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2668
    R-Factor(R-Work) 0.1674
    R-Factor(R-Free) 0.2106
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4084
    Shell Resolution(Low) 2.5048
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2695
    R-Factor(R-Work) 0.1646
    R-Factor(R-Free) 0.1823
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5048
    Shell Resolution(Low) 2.6188
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2702
    R-Factor(R-Work) 0.1621
    R-Factor(R-Free) 0.2072
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6188
    Shell Resolution(Low) 2.7567
    Number of Reflections(R-Free) 124
    Number of Reflections(R-Work) 2723
    R-Factor(R-Work) 0.1537
    R-Factor(R-Free) 0.1836
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7567
    Shell Resolution(Low) 2.9293
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2700
    R-Factor(R-Work) 0.1552
    R-Factor(R-Free) 0.17
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9293
    Shell Resolution(Low) 3.1552
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2719
    R-Factor(R-Work) 0.1623
    R-Factor(R-Free) 0.2027
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1552
    Shell Resolution(Low) 3.4723
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 2705
    R-Factor(R-Work) 0.1607
    R-Factor(R-Free) 0.2214
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4723
    Shell Resolution(Low) 3.9738
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2745
    R-Factor(R-Work) 0.1491
    R-Factor(R-Free) 0.1527
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9738
    Shell Resolution(Low) 5.0026
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2781
    R-Factor(R-Work) 0.1357
    R-Factor(R-Free) 0.1696
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0026
    Shell Resolution(Low) 29.5804
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2912
    R-Factor(R-Work) 0.2015
    R-Factor(R-Free) 0.2091
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 14.103
    f_plane_restr 0.013
    f_chiral_restr 0.148
    f_angle_d 1.894
    f_bond_d 0.021
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 5000
    Nucleic Acid Atoms 0
    Heterogen Atoms 26
    Solvent Atoms 450
     
     
  •   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: 1.7.1_743)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7.1_743)
    model building MOLREP
    data collection DNA