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X-RAY DIFFRACTION
Materials and Methods page
4LD9
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION
    pH 6.5
    Temperature 293.15
    Details 50 mM MES pH 6.5, 12% PEG 400, 12 mM MnCl2, 100 mM NaCl, 10 mM EDTA, VAPOR DIFFUSION, temperature 293.15K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 105.51 α = 90
    b = 105.51 β = 90
    c = 488.23 γ = 120
     
    Space Group
    Space Group Name:    P 61
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 77
     
    Diffraction Detector
    Detector PIXEL
    Type PSI PILATUS 6M
    Collection Date 2013-05-25
     
    Diffraction Radiation
    Monochromator don't know.
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type DIAMOND BEAMLINE I24
    Wavelength List 0.96863
    Site DIAMOND
    Beamline I24
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 3.0
    Observed Criterion Sigma(I) 3.0
    Resolution(High) 3.2
    Resolution(Low) 30
    Number Reflections(All) 44335
    Number Reflections(Observed) 44335
    Percent Possible(Observed) 90.0
     
     
  •   Refinement Hide
    Refinement Statistics
    reflnsShellList 3.306
    Resolution(Low) 19.997
    Cut-off Sigma(F) 1.99
    Number of Reflections(Observed) 44335
    Number of Reflections(R-Free) 2217
    Percent Reflections(Observed) 97.51
    R-Factor(Observed) 0.2405
    R-Work 0.2376
    R-Free 0.2946
     
    Temperature Factor Modeling
    Data Not Available
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3062
    Shell Resolution(Low) 3.3777
    Number of Reflections(R-Free) 123
    Number of Reflections(R-Work) 2371
    R-Factor(R-Work) 0.4072
    R-Factor(R-Free) 0.4257
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3777
    Shell Resolution(Low) 3.4559
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2661
    R-Factor(R-Work) 0.3667
    R-Factor(R-Free) 0.4161
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4559
    Shell Resolution(Low) 3.5419
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2616
    R-Factor(R-Work) 0.3592
    R-Factor(R-Free) 0.3957
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5419
    Shell Resolution(Low) 3.6371
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2667
    R-Factor(R-Work) 0.3292
    R-Factor(R-Free) 0.3606
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6371
    Shell Resolution(Low) 3.7434
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2659
    R-Factor(R-Work) 0.3282
    R-Factor(R-Free) 0.3624
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7434
    Shell Resolution(Low) 3.8634
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2636
    R-Factor(R-Work) 0.3209
    R-Factor(R-Free) 0.3769
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8634
    Shell Resolution(Low) 4.0004
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2669
    R-Factor(R-Work) 0.2984
    R-Factor(R-Free) 0.3905
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0004
    Shell Resolution(Low) 4.1592
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2677
    R-Factor(R-Work) 0.2824
    R-Factor(R-Free) 0.3239
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1592
    Shell Resolution(Low) 4.3467
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2663
    R-Factor(R-Work) 0.2702
    R-Factor(R-Free) 0.3352
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3467
    Shell Resolution(Low) 4.5733
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2704
    R-Factor(R-Work) 0.2438
    R-Factor(R-Free) 0.3458
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5733
    Shell Resolution(Low) 4.856
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2630
    R-Factor(R-Work) 0.231
    R-Factor(R-Free) 0.2792
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.856
    Shell Resolution(Low) 5.2247
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2682
    R-Factor(R-Work) 0.2421
    R-Factor(R-Free) 0.3229
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2247
    Shell Resolution(Low) 5.7392
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2653
    R-Factor(R-Work) 0.237
    R-Factor(R-Free) 0.3176
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.7392
    Shell Resolution(Low) 6.544
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2663
    R-Factor(R-Work) 0.2462
    R-Factor(R-Free) 0.3206
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.544
    Shell Resolution(Low) 8.1508
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2620
    R-Factor(R-Work) 0.2165
    R-Factor(R-Free) 0.2518
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.1508
    Shell Resolution(Low) 19.9969
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2547
    R-Factor(R-Work) 0.1419
    R-Factor(R-Free) 0.1914
    Percent Reflections(Observed) 94.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.006
    f_chiral_restr 0.093
    f_dihedral_angle_d 28.492
    f_angle_d 1.597
    f_bond_d 0.011
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 9299
    Nucleic Acid Atoms 5841
    Heterogen Atoms 0
    Solvent Atoms 0
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution PHASES
    Structure Refinement PHENIX (phenix.refine: 1.8.2_1309)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.8.2_1309)
    model building PHASES