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X-RAY DIFFRACTION
Materials and Methods page
4DA4
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 4.5
    Temperature 277.0
    Details 3 mM TCEP, 0.1 M sodium citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 89.68 α = 90
    b = 152.04 β = 94.54
    c = 96.05 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2011-06-12
     
    Diffraction Radiation
    Monochromator Si mirrors
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 24-ID-E
    Wavelength List 0.9792
    Site APS
    Beamline 24-ID-E
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) -3.0
    Observed Criterion Sigma(I) -1.0
    Resolution(High) 2.6
    Resolution(Low) 50
    Number Reflections(All) 78812
    Number Reflections(Observed) 77126
    Percent Possible(Observed) 97.9
    Redundancy 2.7
     
    High Resolution Shell Details
    Resolution(High) 2.6
    Resolution(Low) 2.69
    Percent Possible(All) 98.0
    Mean I Over Sigma(Observed) 1.9
    R-Sym I(Observed) 0.474
    Redundancy 2.5
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.6
    Resolution(Low) 39.47
    Cut-off Sigma(F) 1.38
    Number of Reflections(all) 78812
    Number of Reflections(Observed) 77070
    Number of Reflections(R-Free) 3882
    Percent Reflections(Observed) 97.8
    R-Factor(Observed) 0.198
    R-Work 0.196
    R-Free 0.246
     
    Temperature Factor Modeling
    Anisotropic B[1][1] 12.3146
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 1.4507
    Anisotropic B[2][2] -6.5241
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -5.7905
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6
    Shell Resolution(Low) 2.6308
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2524
    R-Factor(R-Work) 0.2997
    R-Factor(R-Free) 0.3395
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6308
    Shell Resolution(Low) 2.6641
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2588
    R-Factor(R-Work) 0.3091
    R-Factor(R-Free) 0.3539
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6641
    Shell Resolution(Low) 2.6991
    Number of Reflections(R-Free) 126
    Number of Reflections(R-Work) 2623
    R-Factor(R-Work) 0.2891
    R-Factor(R-Free) 0.4005
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6991
    Shell Resolution(Low) 2.7361
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2647
    R-Factor(R-Work) 0.2897
    R-Factor(R-Free) 0.3441
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7361
    Shell Resolution(Low) 2.7752
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2596
    R-Factor(R-Work) 0.2644
    R-Factor(R-Free) 0.3441
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7752
    Shell Resolution(Low) 2.8166
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2648
    R-Factor(R-Work) 0.2604
    R-Factor(R-Free) 0.3374
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8166
    Shell Resolution(Low) 2.8606
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2609
    R-Factor(R-Work) 0.2602
    R-Factor(R-Free) 0.328
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8606
    Shell Resolution(Low) 2.9075
    Number of Reflections(R-Free) 120
    Number of Reflections(R-Work) 2659
    R-Factor(R-Work) 0.254
    R-Factor(R-Free) 0.2948
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9075
    Shell Resolution(Low) 2.9576
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2614
    R-Factor(R-Work) 0.2426
    R-Factor(R-Free) 0.3451
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9576
    Shell Resolution(Low) 3.0114
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2634
    R-Factor(R-Work) 0.2205
    R-Factor(R-Free) 0.289
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0114
    Shell Resolution(Low) 3.0692
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2610
    R-Factor(R-Work) 0.2088
    R-Factor(R-Free) 0.2925
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0692
    Shell Resolution(Low) 3.1319
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2610
    R-Factor(R-Work) 0.2033
    R-Factor(R-Free) 0.2318
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1319
    Shell Resolution(Low) 3.1999
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2656
    R-Factor(R-Work) 0.1998
    R-Factor(R-Free) 0.251
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1999
    Shell Resolution(Low) 3.2743
    Number of Reflections(R-Free) 121
    Number of Reflections(R-Work) 2633
    R-Factor(R-Work) 0.19
    R-Factor(R-Free) 0.2174
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2743
    Shell Resolution(Low) 3.3562
    Number of Reflections(R-Free) 118
    Number of Reflections(R-Work) 2650
    R-Factor(R-Work) 0.1931
    R-Factor(R-Free) 0.2169
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3562
    Shell Resolution(Low) 3.4469
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 2652
    R-Factor(R-Work) 0.1928
    R-Factor(R-Free) 0.2736
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4469
    Shell Resolution(Low) 3.5482
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2625
    R-Factor(R-Work) 0.1969
    R-Factor(R-Free) 0.2537
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5482
    Shell Resolution(Low) 3.6627
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2599
    R-Factor(R-Work) 0.1946
    R-Factor(R-Free) 0.2521
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6627
    Shell Resolution(Low) 3.7935
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2633
    R-Factor(R-Work) 0.1834
    R-Factor(R-Free) 0.2319
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7935
    Shell Resolution(Low) 3.9453
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2626
    R-Factor(R-Work) 0.1698
    R-Factor(R-Free) 0.2288
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9453
    Shell Resolution(Low) 4.1246
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2628
    R-Factor(R-Work) 0.1523
    R-Factor(R-Free) 0.2223
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1246
    Shell Resolution(Low) 4.3418
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2611
    R-Factor(R-Work) 0.1482
    R-Factor(R-Free) 0.1874
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3418
    Shell Resolution(Low) 4.6135
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 2586
    R-Factor(R-Work) 0.1419
    R-Factor(R-Free) 0.1879
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6135
    Shell Resolution(Low) 4.9691
    Number of Reflections(R-Free) 126
    Number of Reflections(R-Work) 2623
    R-Factor(R-Work) 0.1502
    R-Factor(R-Free) 0.1909
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9691
    Shell Resolution(Low) 5.4679
    Number of Reflections(R-Free) 160
    Number of Reflections(R-Work) 2561
    R-Factor(R-Work) 0.1741
    R-Factor(R-Free) 0.2289
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.4679
    Shell Resolution(Low) 6.2565
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2573
    R-Factor(R-Work) 0.1995
    R-Factor(R-Free) 0.2078
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.2565
    Shell Resolution(Low) 7.8722
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2583
    R-Factor(R-Work) 0.2136
    R-Factor(R-Free) 0.2707
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.8722
    Shell Resolution(Low) 39.467
    Number of Reflections(R-Free) 123
    Number of Reflections(R-Work) 2587
    R-Factor(R-Work) 0.1703
    R-Factor(R-Free) 0.1829
    Percent Reflections(Observed) 94.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.005
    f_chiral_restr 0.088
    f_dihedral_angle_d 17.534
    f_angle_d 1.19
    f_bond_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 13152
    Nucleic Acid Atoms 978
    Heterogen Atoms 69
    Solvent Atoms 860
     
     
  •   Software and Computing Hide
    Computing
    Data Collection MAR345dtb
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHASER
    Structure Refinement PHENIX (PHENIX.REFINE: 1.7.1_743)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7.1_743)
    model building PHASER
    data collection MAR345dtb