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X-RAY DIFFRACTION
Materials and Methods page
4K4V
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    Temperature 289.0
    Details 4.8%(v/v) isopropanol, 0.096 M tacsimate (Hampton Research), 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 dCTP prior to freezing, pH pH 8.5-9.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 63.52 α = 73.48
    b = 63.47 β = 73.44
    c = 101.95 γ = 73.64
     
    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) 2.63
    Resolution(Low) 47.51
    Number Reflections(Observed) 41557
    Percent Possible(Observed) 98.0
    R Merge I(Observed) 0.042
    Redundancy 1.99
     
    High Resolution Shell Details
    Resolution(High) 2.63
    Resolution(Low) 2.72
    Percent Possible(All) 97.7
    R Merge I(Observed) 0.448
    Mean I Over Sigma(Observed) 1.5
    Redundancy 2.0
    Number Unique Reflections(All) 4136
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.63
    Resolution(Low) 47.506
    Cut-off Sigma(F) 1.96
    Number of Reflections(Observed) 41503
    Number of Reflections(R-Free) 2114
    Percent Reflections(Observed) 97.86
    R-Factor(Observed) 0.2349
    R-Work 0.2329
    R-Free 0.2728
     
    Temperature Factor Modeling
    Mean Isotropic B Value 92.7315
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.63
    Shell Resolution(Low) 2.6912
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2556
    R-Factor(R-Work) 0.4282
    R-Factor(R-Free) 0.4593
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6912
    Shell Resolution(Low) 2.7585
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2664
    R-Factor(R-Work) 0.3971
    R-Factor(R-Free) 0.4335
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7585
    Shell Resolution(Low) 2.8331
    Number of Reflections(R-Free) 126
    Number of Reflections(R-Work) 2620
    R-Factor(R-Work) 0.3664
    R-Factor(R-Free) 0.3963
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8331
    Shell Resolution(Low) 2.9164
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2626
    R-Factor(R-Work) 0.3457
    R-Factor(R-Free) 0.3848
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9164
    Shell Resolution(Low) 3.0105
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2628
    R-Factor(R-Work) 0.3349
    R-Factor(R-Free) 0.4118
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0105
    Shell Resolution(Low) 3.1181
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2606
    R-Factor(R-Work) 0.3308
    R-Factor(R-Free) 0.4383
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1181
    Shell Resolution(Low) 3.2429
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2637
    R-Factor(R-Work) 0.3083
    R-Factor(R-Free) 0.3502
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2429
    Shell Resolution(Low) 3.3905
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2657
    R-Factor(R-Work) 0.2912
    R-Factor(R-Free) 0.378
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3905
    Shell Resolution(Low) 3.5692
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 2655
    R-Factor(R-Work) 0.2836
    R-Factor(R-Free) 0.3175
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5692
    Shell Resolution(Low) 3.7927
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2611
    R-Factor(R-Work) 0.2453
    R-Factor(R-Free) 0.3173
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7927
    Shell Resolution(Low) 4.0854
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2614
    R-Factor(R-Work) 0.21
    R-Factor(R-Free) 0.2473
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0854
    Shell Resolution(Low) 4.4962
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2694
    R-Factor(R-Work) 0.1796
    R-Factor(R-Free) 0.2106
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4962
    Shell Resolution(Low) 5.1462
    Number of Reflections(R-Free) 160
    Number of Reflections(R-Work) 2609
    R-Factor(R-Work) 0.186
    R-Factor(R-Free) 0.2291
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1462
    Shell Resolution(Low) 6.481
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2637
    R-Factor(R-Work) 0.1995
    R-Factor(R-Free) 0.2258
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.481
    Shell Resolution(Low) 47.5133
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 2575
    R-Factor(R-Work) 0.2112
    R-Factor(R-Free) 0.2251
    Percent Reflections(Observed) 95.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 18.173
    f_plane_restr 0.007
    f_chiral_restr 0.054
    f_angle_d 1.287
    f_bond_d 0.01
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 7406
    Nucleic Acid Atoms 980
    Heterogen Atoms 10
    Solvent Atoms 44
     
     
  •   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