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X-RAY DIFFRACTION
Materials and Methods page
4EUA
  •   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 = 67.39 α = 90
    b = 110.48 β = 90
    c = 119.16 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 300 mm CCD
    Collection Date 2011-07-24
     
    Diffraction Radiation
    Monochromator Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 21-ID-D
    Wavelength List 1.9075
    Site APS
    Beamline 21-ID-D
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.4
    Resolution(Low) 50
    Number Reflections(All) 34893
    Number Reflections(Observed) 34893
    Percent Possible(Observed) 98.2
    R Merge I(Observed) 0.063
    Redundancy 5.8
     
    High Resolution Shell Details
    Resolution(High) 2.4
    Resolution(Low) 2.49
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.109
    Mean I Over Sigma(Observed) 33.5
    R-Sym I(Observed) 0.109
    Redundancy 5.7
    Number Unique Reflections(All) 3477
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.398
    Resolution(Low) 44.636
    Cut-off Sigma(F) 0.0
    Number of Reflections(R-Free) 3330
    Percent Reflections(Observed) 97.48
    R-Factor(Observed) 0.1551
    R-Work 0.1522
    R-Free 0.2086
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 17.2142
    Anisotropic B[1][1] -1.5041
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 5.2349
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -3.7308
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3984
    Shell Resolution(Low) 2.4326
    Number of Reflections(Observed) 2558
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2409
    R-Factor(R-Work) 0.1525
    R-Factor(R-Free) 0.2364
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4326
    Shell Resolution(Low) 2.4689
    Number of Reflections(Observed) 2781
    Number of Reflections(R-Free) 173
    Number of Reflections(R-Work) 2608
    R-Factor(R-Work) 0.16
    R-Factor(R-Free) 0.2404
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4689
    Shell Resolution(Low) 2.5075
    Number of Reflections(Observed) 2785
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2651
    R-Factor(R-Work) 0.1739
    R-Factor(R-Free) 0.3017
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5075
    Shell Resolution(Low) 2.5486
    Number of Reflections(Observed) 2810
    Number of Reflections(R-Free) 118
    Number of Reflections(R-Work) 2692
    R-Factor(R-Work) 0.1684
    R-Factor(R-Free) 0.2407
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5486
    Shell Resolution(Low) 2.5925
    Number of Reflections(Observed) 2806
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2676
    R-Factor(R-Work) 0.1766
    R-Factor(R-Free) 0.2709
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5925
    Shell Resolution(Low) 2.6397
    Number of Reflections(Observed) 2789
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2652
    R-Factor(R-Work) 0.1609
    R-Factor(R-Free) 0.2615
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6397
    Shell Resolution(Low) 2.6905
    Number of Reflections(Observed) 2802
    Number of Reflections(R-Free) 156
    Number of Reflections(R-Work) 2646
    R-Factor(R-Work) 0.1651
    R-Factor(R-Free) 0.2463
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6905
    Shell Resolution(Low) 2.7454
    Number of Reflections(Observed) 2755
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2611
    R-Factor(R-Work) 0.1581
    R-Factor(R-Free) 0.2205
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7454
    Shell Resolution(Low) 2.805
    Number of Reflections(Observed) 2775
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2629
    R-Factor(R-Work) 0.1658
    R-Factor(R-Free) 0.1997
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.805
    Shell Resolution(Low) 2.8703
    Number of Reflections(Observed) 2734
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2600
    R-Factor(R-Work) 0.1596
    R-Factor(R-Free) 0.24
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8703
    Shell Resolution(Low) 2.9421
    Number of Reflections(Observed) 2837
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2694
    R-Factor(R-Work) 0.1653
    R-Factor(R-Free) 0.2343
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9421
    Shell Resolution(Low) 3.0216
    Number of Reflections(Observed) 2719
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2578
    R-Factor(R-Work) 0.1751
    R-Factor(R-Free) 0.2664
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0216
    Shell Resolution(Low) 3.1105
    Number of Reflections(Observed) 2755
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2625
    R-Factor(R-Work) 0.1801
    R-Factor(R-Free) 0.281
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1105
    Shell Resolution(Low) 3.2108
    Number of Reflections(Observed) 2779
    Number of Reflections(R-Free) 128
    Number of Reflections(R-Work) 2651
    R-Factor(R-Work) 0.1717
    R-Factor(R-Free) 0.2423
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2108
    Shell Resolution(Low) 3.3256
    Number of Reflections(Observed) 2732
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2588
    R-Factor(R-Work) 0.1574
    R-Factor(R-Free) 0.2289
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3256
    Shell Resolution(Low) 3.4587
    Number of Reflections(Observed) 2720
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2584
    R-Factor(R-Work) 0.152
    R-Factor(R-Free) 0.2121
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4587
    Shell Resolution(Low) 3.616
    Number of Reflections(Observed) 2729
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2592
    R-Factor(R-Work) 0.1547
    R-Factor(R-Free) 0.2078
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.616
    Shell Resolution(Low) 3.8066
    Number of Reflections(Observed) 2713
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2577
    R-Factor(R-Work) 0.1431
    R-Factor(R-Free) 0.1822
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8066
    Shell Resolution(Low) 4.0449
    Number of Reflections(Observed) 2731
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2594
    R-Factor(R-Work) 0.1281
    R-Factor(R-Free) 0.1566
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0449
    Shell Resolution(Low) 4.357
    Number of Reflections(Observed) 2654
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2505
    R-Factor(R-Work) 0.1196
    R-Factor(R-Free) 0.1595
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.357
    Shell Resolution(Low) 4.795
    Number of Reflections(Observed) 2711
    Number of Reflections(R-Free) 118
    Number of Reflections(R-Work) 2593
    R-Factor(R-Work) 0.1122
    R-Factor(R-Free) 0.1403
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.795
    Shell Resolution(Low) 5.4877
    Number of Reflections(Observed) 2653
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2513
    R-Factor(R-Work) 0.1237
    R-Factor(R-Free) 0.1468
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.4877
    Shell Resolution(Low) 6.9098
    Number of Reflections(Observed) 2671
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2541
    R-Factor(R-Work) 0.1596
    R-Factor(R-Free) 0.1815
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.9098
    Shell Resolution(Low) 44.6438
    Number of Reflections(Observed) 2607
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2467
    R-Factor(R-Work) 0.167
    R-Factor(R-Free) 0.1777
    Percent Reflections(Observed) 93.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 15.148
    f_plane_restr 0.005
    f_chiral_restr 0.068
    f_angle_d 1.023
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 7764
    Nucleic Acid Atoms 0
    Heterogen Atoms 100
    Solvent Atoms 500
     
     
  •   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