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X-RAY DIFFRACTION
Materials and Methods page
4GZZ
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion, hanging drop
    pH 6.2
    Temperature 295.0
    Details 5-7% PEG 3000, 0.1M MES pH 6.1-6.3, 0.3M LiCl, 10mM MgCl2, vapor diffusion, hanging drop, temperature 295K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 286.55 α = 90
    b = 286.55 β = 90
    c = 199.41 γ = 120
     
    Space Group
    Space Group Name:    H 3
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315r
    Collection Date 2011-11-04
     
    Diffraction Radiation
    Monochromator Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 24-ID-C
    Wavelength List 0.91956
    Site APS
    Beamline 24-ID-C
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 2.0
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 4
    Resolution(Low) 45
    Number Reflections(All) 52138
    Number Reflections(Observed) 51877
    Percent Possible(Observed) 99.5
    R Merge I(Observed) 0.442
    Redundancy 5.9
     
    High Resolution Shell Details
    Resolution(High) 4.0
    Resolution(Low) 4.07
    Percent Possible(All) 97.7
    Redundancy 4.8
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 4.2927
    Resolution(Low) 38.785
    Cut-off Sigma(F) 1.96
    Number of Reflections(all) 41681
    Number of Reflections(Observed) 41266
    Number of Reflections(R-Free) 2070
    Percent Reflections(Observed) 99.01
    R-Factor(Observed) 0.237
    R-Work 0.2345
    R-Free 0.2849
     
    Temperature Factor Modeling
    Mean Isotropic B Value 125.919
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2927
    Shell Resolution(Low) 4.3925
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2516
    R-Factor(R-Work) 0.3463
    R-Factor(R-Free) 0.364
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3925
    Shell Resolution(Low) 4.5022
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2579
    R-Factor(R-Work) 0.3317
    R-Factor(R-Free) 0.3291
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5022
    Shell Resolution(Low) 4.6237
    Number of Reflections(R-Free) 117
    Number of Reflections(R-Work) 2639
    R-Factor(R-Work) 0.3042
    R-Factor(R-Free) 0.335
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6237
    Shell Resolution(Low) 4.7595
    Number of Reflections(R-Free) 164
    Number of Reflections(R-Work) 2585
    R-Factor(R-Work) 0.2861
    R-Factor(R-Free) 0.3725
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7595
    Shell Resolution(Low) 4.9129
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2624
    R-Factor(R-Work) 0.2845
    R-Factor(R-Free) 0.2951
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9129
    Shell Resolution(Low) 5.0881
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2641
    R-Factor(R-Work) 0.2736
    R-Factor(R-Free) 0.2978
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0881
    Shell Resolution(Low) 5.2913
    Number of Reflections(R-Free) 124
    Number of Reflections(R-Work) 2622
    R-Factor(R-Work) 0.2761
    R-Factor(R-Free) 0.2888
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2913
    Shell Resolution(Low) 5.5315
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2626
    R-Factor(R-Work) 0.2746
    R-Factor(R-Free) 0.3372
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.5315
    Shell Resolution(Low) 5.8222
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2639
    R-Factor(R-Work) 0.2716
    R-Factor(R-Free) 0.3669
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.8222
    Shell Resolution(Low) 6.1856
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2624
    R-Factor(R-Work) 0.2603
    R-Factor(R-Free) 0.3049
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.1856
    Shell Resolution(Low) 6.661
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2618
    R-Factor(R-Work) 0.2418
    R-Factor(R-Free) 0.3088
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.661
    Shell Resolution(Low) 7.3273
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2649
    R-Factor(R-Work) 0.2145
    R-Factor(R-Free) 0.2744
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.3273
    Shell Resolution(Low) 8.3782
    Number of Reflections(R-Free) 126
    Number of Reflections(R-Work) 2598
    R-Factor(R-Work) 0.1893
    R-Factor(R-Free) 0.2551
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.3782
    Shell Resolution(Low) 10.5207
    Number of Reflections(R-Free) 124
    Number of Reflections(R-Work) 2648
    R-Factor(R-Work) 0.1802
    R-Factor(R-Free) 0.2351
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 10.5207
    Shell Resolution(Low) 38.7867
    Number of Reflections(R-Free) 123
    Number of Reflections(R-Work) 2588
    R-Factor(R-Work) 0.2142
    R-Factor(R-Free) 0.2513
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.005
    f_chiral_restr 0.061
    f_dihedral_angle_d 16.343
    f_angle_d 0.934
    f_bond_d 0.005
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 23534
    Nucleic Acid Atoms 863
    Heterogen Atoms 3
    Solvent Atoms 0
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL
    Data Reduction (data scaling) HKL
    Structure Solution CNS
    Structure Refinement PHENIX (phenix.refine: 1.8_1069)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    molecular replacement CNS
    data reduction HKL