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X-RAY DIFFRACTION
Materials and Methods page
4K4U
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    Temperature 289.0
    Details 4.8%(v/v) isopropanol, 0.096 M tacsimate (Hampton Research), pH 8.5-9.0, 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 prior to freezing, VAPOR DIFFUSION, SITTING DROP, temperature 289K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 63.65 α = 101.08
    b = 63.87 β = 106.22
    c = 105.1 γ = 103.03
     
    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) 2.85
    Resolution(Low) 45.69
    Number Reflections(Observed) 34198
    Percent Possible(Observed) 98.3
    R Merge I(Observed) 0.047
    Redundancy 2.01
     
    High Resolution Shell Details
    Resolution(High) 2.85
    Resolution(Low) 2.95
    Percent Possible(All) 98.1
    R Merge I(Observed) 0.442
    Mean I Over Sigma(Observed) 1.8
    Redundancy 2.02
    Number Unique Reflections(All) 3403
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.85
    Resolution(Low) 43.263
    Cut-off Sigma(F) 1.97
    Number of Reflections(Observed) 34099
    Number of Reflections(R-Free) 1743
    Percent Reflections(Observed) 98.05
    R-Factor(Observed) 0.2216
    R-Work 0.2186
    R-Free 0.2757
     
    Temperature Factor Modeling
    Mean Isotropic B Value 96.6887
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.85
    Shell Resolution(Low) 2.9338
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2692
    R-Factor(R-Work) 0.3582
    R-Factor(R-Free) 0.3788
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9338
    Shell Resolution(Low) 3.0285
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2701
    R-Factor(R-Work) 0.3233
    R-Factor(R-Free) 0.3775
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0285
    Shell Resolution(Low) 3.1367
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2644
    R-Factor(R-Work) 0.2982
    R-Factor(R-Free) 0.3778
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1367
    Shell Resolution(Low) 3.2623
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2699
    R-Factor(R-Work) 0.2815
    R-Factor(R-Free) 0.3164
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2623
    Shell Resolution(Low) 3.4107
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2742
    R-Factor(R-Work) 0.2778
    R-Factor(R-Free) 0.3807
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4107
    Shell Resolution(Low) 3.5904
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2713
    R-Factor(R-Work) 0.2803
    R-Factor(R-Free) 0.3532
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5904
    Shell Resolution(Low) 3.8153
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2688
    R-Factor(R-Work) 0.2934
    R-Factor(R-Free) 0.3945
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8153
    Shell Resolution(Low) 4.1096
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2659
    R-Factor(R-Work) 0.2134
    R-Factor(R-Free) 0.276
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1096
    Shell Resolution(Low) 4.5228
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2754
    R-Factor(R-Work) 0.1753
    R-Factor(R-Free) 0.2195
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5228
    Shell Resolution(Low) 5.1763
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2688
    R-Factor(R-Work) 0.1697
    R-Factor(R-Free) 0.2394
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1763
    Shell Resolution(Low) 6.5181
    Number of Reflections(R-Free) 161
    Number of Reflections(R-Work) 2723
    R-Factor(R-Work) 0.1925
    R-Factor(R-Free) 0.2726
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.5181
    Shell Resolution(Low) 43.2675
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2653
    R-Factor(R-Work) 0.1925
    R-Factor(R-Free) 0.2112
    Percent Reflections(Observed) 97.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 16.781
    f_plane_restr 0.007
    f_chiral_restr 0.049
    f_angle_d 1.253
    f_bond_d 0.009
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 7406
    Nucleic Acid Atoms 1544
    Heterogen Atoms 20
    Solvent Atoms 57
     
     
  •   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: 9.9.9.4D
    data collection D*trek