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X-RAY DIFFRACTION
Materials and Methods page
4H4G
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 8.5
    Temperature 289.0
    Details 10% w/v PEG 20 000, 20% v/v PEG MME 550, 0.02 M of each carboxylic acid, 0.1 M bicine/Trizma base pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 136.37 α = 90
    b = 136.37 β = 90
    c = 364.52 γ = 120
     
    Space Group
    Space Group Name:    P 61 2 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MAR scanner 300 mm plate
    Collection Date 2012-07-20
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 21-ID-F
    Wavelength List 0.97872
    Site APS
    Beamline 21-ID-F
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 2.0
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 2.65
    Resolution(Low) 50
    Number Reflections(All) 220240
    Number Reflections(Observed) 218698
    Percent Possible(Observed) 99.3
    R Merge I(Observed) 0.084
    B(Isotropic) From Wilson Plot 45.565
     
    High Resolution Shell Details
    Resolution(High) 2.65
    Resolution(Low) 2.72
    Percent Possible(All) 99.6
    R Merge I(Observed) 0.428
    Mean I Over Sigma(Observed) 2.84
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.65
    Resolution(Low) 49.556
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 60755
    Number of Reflections(Observed) 57852
    Number of Reflections(R-Free) 2903
    Percent Reflections(Observed) 97.89
    R-Factor(Observed) 0.1874
    R-Work 0.1843
    R-Free 0.2468
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 28.6234
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.65
    Shell Resolution(Low) 2.6934
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2438
    R-Factor(R-Work) 0.2007
    R-Factor(R-Free) 0.2896
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6934
    Shell Resolution(Low) 2.7398
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2471
    R-Factor(R-Work) 0.2094
    R-Factor(R-Free) 0.3053
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7398
    Shell Resolution(Low) 2.7897
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2480
    R-Factor(R-Work) 0.2148
    R-Factor(R-Free) 0.3638
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7897
    Shell Resolution(Low) 2.8433
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2524
    R-Factor(R-Work) 0.2036
    R-Factor(R-Free) 0.2823
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8433
    Shell Resolution(Low) 2.9013
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2528
    R-Factor(R-Work) 0.2037
    R-Factor(R-Free) 0.3123
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9013
    Shell Resolution(Low) 2.9644
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2551
    R-Factor(R-Work) 0.2193
    R-Factor(R-Free) 0.3037
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9644
    Shell Resolution(Low) 3.0334
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2544
    R-Factor(R-Work) 0.2109
    R-Factor(R-Free) 0.2937
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0334
    Shell Resolution(Low) 3.1092
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2583
    R-Factor(R-Work) 0.2088
    R-Factor(R-Free) 0.3232
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1092
    Shell Resolution(Low) 3.1933
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2560
    R-Factor(R-Work) 0.2014
    R-Factor(R-Free) 0.2385
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1933
    Shell Resolution(Low) 3.2872
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2587
    R-Factor(R-Work) 0.1918
    R-Factor(R-Free) 0.2639
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2872
    Shell Resolution(Low) 3.3933
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2616
    R-Factor(R-Work) 0.1971
    R-Factor(R-Free) 0.2704
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3933
    Shell Resolution(Low) 3.5145
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2614
    R-Factor(R-Work) 0.1944
    R-Factor(R-Free) 0.2458
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5145
    Shell Resolution(Low) 3.6552
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2625
    R-Factor(R-Work) 0.1909
    R-Factor(R-Free) 0.2714
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6552
    Shell Resolution(Low) 3.8215
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2638
    R-Factor(R-Work) 0.1719
    R-Factor(R-Free) 0.218
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8215
    Shell Resolution(Low) 4.0229
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2675
    R-Factor(R-Work) 0.1724
    R-Factor(R-Free) 0.2213
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0229
    Shell Resolution(Low) 4.2748
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2678
    R-Factor(R-Work) 0.1521
    R-Factor(R-Free) 0.2354
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2748
    Shell Resolution(Low) 4.6047
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2677
    R-Factor(R-Work) 0.1309
    R-Factor(R-Free) 0.1791
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6047
    Shell Resolution(Low) 5.0677
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2711
    R-Factor(R-Work) 0.1398
    R-Factor(R-Free) 0.1886
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0677
    Shell Resolution(Low) 5.8
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2736
    R-Factor(R-Work) 0.1821
    R-Factor(R-Free) 0.2315
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.8
    Shell Resolution(Low) 7.3036
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2776
    R-Factor(R-Work) 0.2121
    R-Factor(R-Free) 0.2793
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.3036
    Shell Resolution(Low) 49.5645
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2937
    R-Factor(R-Work) 0.213
    R-Factor(R-Free) 0.227
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 14.043
    f_plane_restr 0.007
    f_chiral_restr 0.083
    f_angle_d 1.552
    f_bond_d 0.014
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 9169
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 104
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-3000
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.8_1069)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    molecular replacement Phaser
    data reduction Xscale