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X-RAY DIFFRACTION
Materials and Methods page
4EUB
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 8.2
    Temperature 298.0
    Details 0.9 M sodium citrate, 0.1 M imidazole, 25 mM 2-mercaptoethanol, and 2 mM succinyl-CoA, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 67.4 α = 90
    b = 110.28 β = 90
    c = 120.24 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 225 mm CCD
    Collection Date 2011-07-23
     
    Diffraction Radiation
    Monochromator C(111)
    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(I) -3.0
    Resolution(High) 1.97
    Resolution(Low) 50
    Number Reflections(All) 63807
    Number Reflections(Observed) 63807
    Percent Possible(Observed) 100.0
    R Merge I(Observed) 0.12
    Redundancy 14.2
     
    High Resolution Shell Details
    Resolution(High) 1.97
    Resolution(Low) 2.0
    Percent Possible(All) 99.9
    R Merge I(Observed) 0.491
    Mean I Over Sigma(Observed) 6.3
    R-Sym I(Observed) 0.491
    Redundancy 13.4
    Number Unique Reflections(All) 3167
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.973
    Resolution(Low) 40.22
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 63732
    Number of Reflections(R-Free) 3179
    Percent Reflections(Observed) 99.84
    R-Factor(Observed) 0.1569
    R-Work 0.1542
    R-Free 0.2089
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 18.5026
    Anisotropic B[1][1] 4.7659
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.08
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -4.6859
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9726
    Shell Resolution(Low) 2.002
    Number of Reflections(Observed) 2654
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2524
    R-Factor(R-Work) 0.1816
    R-Factor(R-Free) 0.2636
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.002
    Shell Resolution(Low) 2.0333
    Number of Reflections(Observed) 2728
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2591
    R-Factor(R-Work) 0.1707
    R-Factor(R-Free) 0.2277
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0333
    Shell Resolution(Low) 2.0666
    Number of Reflections(Observed) 2717
    Number of Reflections(R-Free) 123
    Number of Reflections(R-Work) 2594
    R-Factor(R-Work) 0.1788
    R-Factor(R-Free) 0.2483
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0666
    Shell Resolution(Low) 2.1023
    Number of Reflections(Observed) 2754
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2606
    R-Factor(R-Work) 0.1782
    R-Factor(R-Free) 0.2713
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1023
    Shell Resolution(Low) 2.1405
    Number of Reflections(Observed) 2722
    Number of Reflections(R-Free) 128
    Number of Reflections(R-Work) 2594
    R-Factor(R-Work) 0.1665
    R-Factor(R-Free) 0.2703
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1405
    Shell Resolution(Low) 2.1817
    Number of Reflections(Observed) 2788
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2652
    R-Factor(R-Work) 0.1605
    R-Factor(R-Free) 0.2383
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1817
    Shell Resolution(Low) 2.2262
    Number of Reflections(Observed) 2736
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2593
    R-Factor(R-Work) 0.1655
    R-Factor(R-Free) 0.2472
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2262
    Shell Resolution(Low) 2.2746
    Number of Reflections(Observed) 2726
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2577
    R-Factor(R-Work) 0.1753
    R-Factor(R-Free) 0.2418
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2746
    Shell Resolution(Low) 2.3275
    Number of Reflections(Observed) 2763
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2618
    R-Factor(R-Work) 0.1709
    R-Factor(R-Free) 0.2608
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3275
    Shell Resolution(Low) 2.3857
    Number of Reflections(Observed) 2731
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2601
    R-Factor(R-Work) 0.1681
    R-Factor(R-Free) 0.2531
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3857
    Shell Resolution(Low) 2.4502
    Number of Reflections(Observed) 2777
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 2650
    R-Factor(R-Work) 0.1629
    R-Factor(R-Free) 0.2156
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4502
    Shell Resolution(Low) 2.5223
    Number of Reflections(Observed) 2754
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2608
    R-Factor(R-Work) 0.1589
    R-Factor(R-Free) 0.2067
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5223
    Shell Resolution(Low) 2.6037
    Number of Reflections(Observed) 2758
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2613
    R-Factor(R-Work) 0.1565
    R-Factor(R-Free) 0.1981
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6037
    Shell Resolution(Low) 2.6967
    Number of Reflections(Observed) 2756
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2625
    R-Factor(R-Work) 0.1654
    R-Factor(R-Free) 0.2282
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6967
    Shell Resolution(Low) 2.8047
    Number of Reflections(Observed) 2769
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2635
    R-Factor(R-Work) 0.176
    R-Factor(R-Free) 0.2515
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8047
    Shell Resolution(Low) 2.9323
    Number of Reflections(Observed) 2779
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2637
    R-Factor(R-Work) 0.1646
    R-Factor(R-Free) 0.2105
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9323
    Shell Resolution(Low) 3.0868
    Number of Reflections(Observed) 2768
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 2643
    R-Factor(R-Work) 0.1683
    R-Factor(R-Free) 0.2331
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0868
    Shell Resolution(Low) 3.2801
    Number of Reflections(Observed) 2783
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2631
    R-Factor(R-Work) 0.1547
    R-Factor(R-Free) 0.2009
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2801
    Shell Resolution(Low) 3.5332
    Number of Reflections(Observed) 2805
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2673
    R-Factor(R-Work) 0.1469
    R-Factor(R-Free) 0.1796
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5332
    Shell Resolution(Low) 3.8886
    Number of Reflections(Observed) 2793
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2648
    R-Factor(R-Work) 0.1336
    R-Factor(R-Free) 0.1843
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8886
    Shell Resolution(Low) 4.4506
    Number of Reflections(Observed) 2832
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2694
    R-Factor(R-Work) 0.1256
    R-Factor(R-Free) 0.1562
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4506
    Shell Resolution(Low) 5.6049
    Number of Reflections(Observed) 2856
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2710
    R-Factor(R-Work) 0.1263
    R-Factor(R-Free) 0.1704
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.6049
    Shell Resolution(Low) 40.2281
    Number of Reflections(Observed) 2983
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2836
    R-Factor(R-Work) 0.14
    R-Factor(R-Free) 0.171
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 15.272
    f_plane_restr 0.005
    f_chiral_restr 0.07
    f_angle_d 1.067
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 7676
    Nucleic Acid Atoms 0
    Heterogen Atoms 100
    Solvent Atoms 795
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHENIX
    Structure Refinement PHENIX (phenix.refine: 1.7.1_743)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction HKL