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X-RAY DIFFRACTION
Materials and Methods page
3QX3
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5.8
    Temperature 277.0
    Details 0.1M magnesium acetate, 50mM 2-(N-morpholino)ethanesulfonic acid pH 5.8, 22% 2-methyl-2, 4-pentanediol (MPT), VAPOR DIFFUSION, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 80.15 α = 90
    b = 176.8 β = 111.58
    c = 94.07 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 210
    Collection Date 2010-12-02
     
    Diffraction Radiation
    Monochromator Fixed-Exit Double Crystal Monochromator (Crystal type Si(1 1 1))
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SPRING-8 BEAMLINE BL12B2
    Wavelength List 0.90000
    Site SPRING-8
    Beamline BL12B2
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 1.0
    Observed Criterion Sigma(I) 1.0
    Resolution(High) 2.16
    Resolution(Low) 30
    Number Reflections(All) 123847
    Number Reflections(Observed) 129411
    Percent Possible(Observed) 95.7
    B(Isotropic) From Wilson Plot 32.09
    Redundancy 2.6
     
    High Resolution Shell Details
    Resolution(High) 2.16
    Resolution(Low) 2.2
    Percent Possible(All) 98.2
    R Merge I(Observed) 0.472
    Mean I Over Sigma(Observed) 2.1
    R-Sym I(Observed) 0.472
    Redundancy 2.3
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.162
    Resolution(Low) 29.543
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 129619
    Number of Reflections(Observed) 117720
    Number of Reflections(R-Free) 5917
    Percent Reflections(Observed) 90.82
    R-Factor(Observed) 0.1701
    R-Work 0.1682
    R-Free 0.2072
     
    Temperature Factor Modeling
    Mean Isotropic B Value 37.0272
    Anisotropic B[1][1] 6.3155
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 5.9953
    Anisotropic B[2][2] 1.0717
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 3.9119
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1619
    Shell Resolution(Low) 2.2391
    Number of Reflections(R-Free) 572
    Number of Reflections(R-Work) 10113
    R-Factor(R-Work) 0.2325
    R-Factor(R-Free) 0.2882
    Percent Reflections(Observed) 82.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2391
    Shell Resolution(Low) 2.3288
    Number of Reflections(R-Free) 537
    Number of Reflections(R-Work) 10652
    R-Factor(R-Work) 0.2097
    R-Factor(R-Free) 0.2689
    Percent Reflections(Observed) 87.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3288
    Shell Resolution(Low) 2.4347
    Number of Reflections(R-Free) 576
    Number of Reflections(R-Work) 11012
    R-Factor(R-Work) 0.1945
    R-Factor(R-Free) 0.2482
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4347
    Shell Resolution(Low) 2.563
    Number of Reflections(R-Free) 576
    Number of Reflections(R-Work) 11223
    R-Factor(R-Work) 0.1902
    R-Factor(R-Free) 0.2316
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.563
    Shell Resolution(Low) 2.7235
    Number of Reflections(R-Free) 574
    Number of Reflections(R-Work) 11420
    R-Factor(R-Work) 0.1781
    R-Factor(R-Free) 0.2357
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7235
    Shell Resolution(Low) 2.9336
    Number of Reflections(R-Free) 630
    Number of Reflections(R-Work) 11577
    R-Factor(R-Work) 0.1712
    R-Factor(R-Free) 0.2131
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9336
    Shell Resolution(Low) 3.2285
    Number of Reflections(R-Free) 652
    Number of Reflections(R-Work) 11605
    R-Factor(R-Work) 0.1656
    R-Factor(R-Free) 0.2181
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2285
    Shell Resolution(Low) 3.6949
    Number of Reflections(R-Free) 594
    Number of Reflections(R-Work) 11700
    R-Factor(R-Work) 0.1513
    R-Factor(R-Free) 0.1895
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6949
    Shell Resolution(Low) 4.6522
    Number of Reflections(R-Free) 625
    Number of Reflections(R-Work) 11317
    R-Factor(R-Work) 0.1397
    R-Factor(R-Free) 0.1686
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6522
    Shell Resolution(Low) 29.5462
    Number of Reflections(R-Free) 581
    Number of Reflections(R-Work) 11184
    R-Factor(R-Work) 0.1726
    R-Factor(R-Free) 0.1982
    Percent Reflections(Observed) 90.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.004
    f_chiral_restr 0.069
    f_dihedral_angle_d 15.442
    f_angle_d 1.058
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 10826
    Nucleic Acid Atoms 820
    Heterogen Atoms 90
    Solvent Atoms 1047
     
     
  •   Software and Computing Hide
    Computing
    Data Collection bluice
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHENIX (phenix.automr: 1.6.4_486)
    Structure Refinement PHENIX (phenix.refine: 1.7_650)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.6.4_486)
    model building PHENIX version: (phenix.automr: 1.6.4_486)
    data collection bluice