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X-RAY DIFFRACTION
Materials and Methods page
4K4W
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    Temperature 289.0
    Details 4.8%(v/v) isopropanol, 0.096 M tacsimate, 1.92-1.95 M ammonium sulfate, and 10-11%(v/v) glycerol and then gradually exchanged into a cryo stabilizer solution containing 4.8%(v/v) isopropanol, 0.096 M tacsimate, 1.95 M ammonium sulfate and 19-27%(v/v) xylitol with CTP prior to freezing, VAPOR DIFFUSION, SITTING DROP, temperature 289K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 64.49 α = 73.65
    b = 64.37 β = 73.56
    c = 102.29 γ = 72.2
     
    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) 2.0
    Observed Criterion Sigma(I) 1.5
    Resolution(High) 2.69
    Resolution(Low) 42.38
    Number Reflections(Observed) 39877
    Percent Possible(Observed) 97.9
    R Merge I(Observed) 0.05
    Redundancy 1.99
     
    High Resolution Shell Details
    Resolution(High) 2.69
    Resolution(Low) 2.79
    Percent Possible(All) 98.0
    R Merge I(Observed) 0.456
    Mean I Over Sigma(Observed) 1.5
    Redundancy 1.98
    Number Unique Reflections(All) 3951
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.69
    Resolution(Low) 42.376
    Cut-off Sigma(F) 1.96
    Number of Reflections(Observed) 39801
    Number of Reflections(R-Free) 2022
    Percent Reflections(Observed) 97.75
    R-Factor(Observed) 0.2151
    R-Work 0.2128
    R-Free 0.2562
     
    Temperature Factor Modeling
    Mean Isotropic B Value 81.9612
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.69
    Shell Resolution(Low) 2.7573
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2662
    R-Factor(R-Work) 0.3429
    R-Factor(R-Free) 0.3472
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7573
    Shell Resolution(Low) 2.8318
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2752
    R-Factor(R-Work) 0.3269
    R-Factor(R-Free) 0.3969
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8318
    Shell Resolution(Low) 2.9151
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2733
    R-Factor(R-Work) 0.3137
    R-Factor(R-Free) 0.3333
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9151
    Shell Resolution(Low) 3.0092
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2662
    R-Factor(R-Work) 0.2989
    R-Factor(R-Free) 0.364
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0092
    Shell Resolution(Low) 3.1167
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2721
    R-Factor(R-Work) 0.2983
    R-Factor(R-Free) 0.3751
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1167
    Shell Resolution(Low) 3.2415
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 2724
    R-Factor(R-Work) 0.2891
    R-Factor(R-Free) 0.3666
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2415
    Shell Resolution(Low) 3.3889
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2749
    R-Factor(R-Work) 0.2659
    R-Factor(R-Free) 0.3197
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3889
    Shell Resolution(Low) 3.5675
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 2660
    R-Factor(R-Work) 0.278
    R-Factor(R-Free) 0.2972
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5675
    Shell Resolution(Low) 3.7909
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2680
    R-Factor(R-Work) 0.2621
    R-Factor(R-Free) 0.3236
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7909
    Shell Resolution(Low) 4.0834
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2598
    R-Factor(R-Work) 0.2028
    R-Factor(R-Free) 0.2642
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0834
    Shell Resolution(Low) 4.4939
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2747
    R-Factor(R-Work) 0.1624
    R-Factor(R-Free) 0.2019
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4939
    Shell Resolution(Low) 5.1432
    Number of Reflections(R-Free) 164
    Number of Reflections(R-Work) 2691
    R-Factor(R-Work) 0.1659
    R-Factor(R-Free) 0.2166
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1432
    Shell Resolution(Low) 6.4762
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2735
    R-Factor(R-Work) 0.1793
    R-Factor(R-Free) 0.2277
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.4762
    Shell Resolution(Low) 42.3812
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2665
    R-Factor(R-Work) 0.1712
    R-Factor(R-Free) 0.1806
    Percent Reflections(Observed) 96.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 17.722
    f_plane_restr 0.007
    f_chiral_restr 0.049
    f_angle_d 1.217
    f_bond_d 0.009
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 7400
    Nucleic Acid Atoms 1520
    Heterogen Atoms 0
    Solvent Atoms 109
     
     
  •   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: 9.9.9.1L
    data collection D*trek