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X-RAY DIFFRACTION
Materials and Methods page
4K4Y
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 8.5
    Temperature 289.0
    Details 0.17 M sodium acetate, 0.085 M Tris, 25.5% PEG 4000, and 15% glycerol and directly frozen , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 60.37 α = 89.92
    b = 60.4 β = 89.96
    c = 194.03 γ = 79.75
     
    Space Group
    Space Group Name:    P 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type NOIR-1
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ALS BEAMLINE 4.2.2
    Wavelength List 1.00
    Site ALS
    Beamline 4.2.2
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 1.5
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 2.72
    Resolution(Low) 45.06
    Number Reflections(Observed) 70840
    Percent Possible(Observed) 97.8
    R Merge I(Observed) 0.097
    Redundancy 1.92
     
    High Resolution Shell Details
    Resolution(High) 2.72
    Resolution(Low) 2.82
    Percent Possible(All) 97.5
    R Merge I(Observed) 0.422
    Mean I Over Sigma(Observed) 1.6
    Redundancy 1.92
    Number Unique Reflections(All) 7013
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.72
    Resolution(Low) 43.762
    Cut-off Sigma(F) 1.96
    Number of Reflections(Observed) 70695
    Number of Reflections(R-Free) 3555
    Percent Reflections(Observed) 97.62
    R-Factor(Observed) 0.2015
    R-Work 0.199
    R-Free 0.2469
     
    Temperature Factor Modeling
    Mean Isotropic B Value 50.9641
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.72
    Shell Resolution(Low) 2.7573
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2673
    R-Factor(R-Work) 0.3092
    R-Factor(R-Free) 0.4028
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7573
    Shell Resolution(Low) 2.7966
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2612
    R-Factor(R-Work) 0.2875
    R-Factor(R-Free) 0.3399
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7966
    Shell Resolution(Low) 2.8384
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2675
    R-Factor(R-Work) 0.2942
    R-Factor(R-Free) 0.366
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8384
    Shell Resolution(Low) 2.8827
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2767
    R-Factor(R-Work) 0.2981
    R-Factor(R-Free) 0.3701
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8827
    Shell Resolution(Low) 2.93
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2580
    R-Factor(R-Work) 0.2906
    R-Factor(R-Free) 0.3591
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.93
    Shell Resolution(Low) 2.9805
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2754
    R-Factor(R-Work) 0.2748
    R-Factor(R-Free) 0.3354
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9805
    Shell Resolution(Low) 3.0347
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2673
    R-Factor(R-Work) 0.2729
    R-Factor(R-Free) 0.3684
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0347
    Shell Resolution(Low) 3.093
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2655
    R-Factor(R-Work) 0.267
    R-Factor(R-Free) 0.3362
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.093
    Shell Resolution(Low) 3.1561
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2726
    R-Factor(R-Work) 0.2525
    R-Factor(R-Free) 0.3193
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1561
    Shell Resolution(Low) 3.2247
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2685
    R-Factor(R-Work) 0.2418
    R-Factor(R-Free) 0.3067
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2247
    Shell Resolution(Low) 3.2997
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2682
    R-Factor(R-Work) 0.259
    R-Factor(R-Free) 0.3077
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2997
    Shell Resolution(Low) 3.3822
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2708
    R-Factor(R-Work) 0.2485
    R-Factor(R-Free) 0.3271
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3822
    Shell Resolution(Low) 3.4736
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2638
    R-Factor(R-Work) 0.213
    R-Factor(R-Free) 0.3054
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4736
    Shell Resolution(Low) 3.5758
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2783
    R-Factor(R-Work) 0.2018
    R-Factor(R-Free) 0.2488
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5758
    Shell Resolution(Low) 3.6912
    Number of Reflections(R-Free) 159
    Number of Reflections(R-Work) 2655
    R-Factor(R-Work) 0.1911
    R-Factor(R-Free) 0.2398
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6912
    Shell Resolution(Low) 3.823
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2659
    R-Factor(R-Work) 0.1733
    R-Factor(R-Free) 0.2164
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.823
    Shell Resolution(Low) 3.976
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 2686
    R-Factor(R-Work) 0.1668
    R-Factor(R-Free) 0.2427
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.976
    Shell Resolution(Low) 4.1568
    Number of Reflections(R-Free) 128
    Number of Reflections(R-Work) 2699
    R-Factor(R-Work) 0.146
    R-Factor(R-Free) 0.1932
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1568
    Shell Resolution(Low) 4.3758
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2711
    R-Factor(R-Work) 0.151
    R-Factor(R-Free) 0.1552
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3758
    Shell Resolution(Low) 4.6496
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2783
    R-Factor(R-Work) 0.1326
    R-Factor(R-Free) 0.1771
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6496
    Shell Resolution(Low) 5.0082
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2686
    R-Factor(R-Work) 0.1553
    R-Factor(R-Free) 0.1844
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0082
    Shell Resolution(Low) 5.5113
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2706
    R-Factor(R-Work) 0.1645
    R-Factor(R-Free) 0.2078
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.5113
    Shell Resolution(Low) 6.3068
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2648
    R-Factor(R-Work) 0.1805
    R-Factor(R-Free) 0.2313
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.3068
    Shell Resolution(Low) 7.9381
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2681
    R-Factor(R-Work) 0.1811
    R-Factor(R-Free) 0.1913
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.9381
    Shell Resolution(Low) 43.7673
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 2615
    R-Factor(R-Work) 0.1825
    R-Factor(R-Free) 0.1827
    Percent Reflections(Observed) 94.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 17.75
    f_plane_restr 0.007
    f_chiral_restr 0.048
    f_angle_d 1.166
    f_bond_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 14772
    Nucleic Acid Atoms 2948
    Heterogen Atoms 192
    Solvent Atoms 372
     
     
  •   Software and Computing Hide
    Computing
    Data Collection BLU-ICE
    Data Reduction (intensity integration) DTREK
    Data Reduction (data scaling) DTREK
    Structure Solution PHENIX
    Structure Refinement PHENIX (phenix.refine: 1.8.2_1309)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction D*trek version: 9.9.8.0L
    data collection D*trek