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X-RAY DIFFRACTION
Materials and Methods page
4EU9
  •   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 = 67.09 α = 90
    b = 110.1 β = 90
    c = 119.84 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) 1.48
    Resolution(Low) 50
    Number Reflections(All) 148137
    Number Reflections(Observed) 148137
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.079
    Redundancy 13.6
     
    High Resolution Shell Details
    Resolution(High) 1.48
    Resolution(Low) 1.51
    Percent Possible(All) 99.8
    R Merge I(Observed) 0.574
    Mean I Over Sigma(Observed) 4.4
    R-Sym I(Observed) 0.574
    Redundancy 12.9
    Number Unique Reflections(All) 7318
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.479
    Resolution(Low) 30.998
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 147934
    Number of Reflections(R-Free) 7386
    Percent Reflections(Observed) 99.83
    R-Factor(Observed) 0.1585
    R-Work 0.1574
    R-Free 0.1792
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 15.2522
    Anisotropic B[1][1] -1.2319
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 3.8218
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -2.5899
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4795
    Shell Resolution(Low) 1.4963
    Number of Reflections(Observed) 4828
    Number of Reflections(R-Free) 232
    Number of Reflections(R-Work) 4596
    R-Factor(R-Work) 0.1914
    R-Factor(R-Free) 0.2213
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4963
    Shell Resolution(Low) 1.5139
    Number of Reflections(Observed) 4828
    Number of Reflections(R-Free) 251
    Number of Reflections(R-Work) 4577
    R-Factor(R-Work) 0.1887
    R-Factor(R-Free) 0.2494
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5139
    Shell Resolution(Low) 1.5324
    Number of Reflections(Observed) 4901
    Number of Reflections(R-Free) 252
    Number of Reflections(R-Work) 4649
    R-Factor(R-Work) 0.1783
    R-Factor(R-Free) 0.2218
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5324
    Shell Resolution(Low) 1.5518
    Number of Reflections(Observed) 4899
    Number of Reflections(R-Free) 254
    Number of Reflections(R-Work) 4645
    R-Factor(R-Work) 0.1711
    R-Factor(R-Free) 0.1952
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5518
    Shell Resolution(Low) 1.5722
    Number of Reflections(Observed) 4873
    Number of Reflections(R-Free) 225
    Number of Reflections(R-Work) 4648
    R-Factor(R-Work) 0.1678
    R-Factor(R-Free) 0.2055
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5722
    Shell Resolution(Low) 1.5937
    Number of Reflections(Observed) 4897
    Number of Reflections(R-Free) 234
    Number of Reflections(R-Work) 4663
    R-Factor(R-Work) 0.167
    R-Factor(R-Free) 0.1926
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5937
    Shell Resolution(Low) 1.6165
    Number of Reflections(Observed) 4881
    Number of Reflections(R-Free) 248
    Number of Reflections(R-Work) 4633
    R-Factor(R-Work) 0.16
    R-Factor(R-Free) 0.1977
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6165
    Shell Resolution(Low) 1.6406
    Number of Reflections(Observed) 4901
    Number of Reflections(R-Free) 238
    Number of Reflections(R-Work) 4663
    R-Factor(R-Work) 0.1594
    R-Factor(R-Free) 0.1997
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6406
    Shell Resolution(Low) 1.6662
    Number of Reflections(Observed) 4869
    Number of Reflections(R-Free) 236
    Number of Reflections(R-Work) 4633
    R-Factor(R-Work) 0.1624
    R-Factor(R-Free) 0.2008
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6662
    Shell Resolution(Low) 1.6936
    Number of Reflections(Observed) 4946
    Number of Reflections(R-Free) 262
    Number of Reflections(R-Work) 4684
    R-Factor(R-Work) 0.1604
    R-Factor(R-Free) 0.1952
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6936
    Shell Resolution(Low) 1.7228
    Number of Reflections(Observed) 4871
    Number of Reflections(R-Free) 222
    Number of Reflections(R-Work) 4649
    R-Factor(R-Work) 0.1535
    R-Factor(R-Free) 0.1757
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7228
    Shell Resolution(Low) 1.7541
    Number of Reflections(Observed) 4877
    Number of Reflections(R-Free) 270
    Number of Reflections(R-Work) 4607
    R-Factor(R-Work) 0.158
    R-Factor(R-Free) 0.2069
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7541
    Shell Resolution(Low) 1.7878
    Number of Reflections(Observed) 4911
    Number of Reflections(R-Free) 254
    Number of Reflections(R-Work) 4657
    R-Factor(R-Work) 0.1579
    R-Factor(R-Free) 0.2038
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7878
    Shell Resolution(Low) 1.8243
    Number of Reflections(Observed) 4906
    Number of Reflections(R-Free) 218
    Number of Reflections(R-Work) 4688
    R-Factor(R-Work) 0.1629
    R-Factor(R-Free) 0.1973
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8243
    Shell Resolution(Low) 1.864
    Number of Reflections(Observed) 4938
    Number of Reflections(R-Free) 257
    Number of Reflections(R-Work) 4681
    R-Factor(R-Work) 0.1602
    R-Factor(R-Free) 0.1906
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.864
    Shell Resolution(Low) 1.9073
    Number of Reflections(Observed) 4897
    Number of Reflections(R-Free) 239
    Number of Reflections(R-Work) 4658
    R-Factor(R-Work) 0.1524
    R-Factor(R-Free) 0.1688
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9073
    Shell Resolution(Low) 1.955
    Number of Reflections(Observed) 4896
    Number of Reflections(R-Free) 261
    Number of Reflections(R-Work) 4635
    R-Factor(R-Work) 0.1572
    R-Factor(R-Free) 0.1872
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.955
    Shell Resolution(Low) 2.0079
    Number of Reflections(Observed) 4921
    Number of Reflections(R-Free) 236
    Number of Reflections(R-Work) 4685
    R-Factor(R-Work) 0.1592
    R-Factor(R-Free) 0.1825
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0079
    Shell Resolution(Low) 2.0669
    Number of Reflections(Observed) 4927
    Number of Reflections(R-Free) 253
    Number of Reflections(R-Work) 4674
    R-Factor(R-Work) 0.1592
    R-Factor(R-Free) 0.1813
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0669
    Shell Resolution(Low) 2.1336
    Number of Reflections(Observed) 4903
    Number of Reflections(R-Free) 231
    Number of Reflections(R-Work) 4672
    R-Factor(R-Work) 0.1552
    R-Factor(R-Free) 0.1789
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1336
    Shell Resolution(Low) 2.2099
    Number of Reflections(Observed) 4924
    Number of Reflections(R-Free) 258
    Number of Reflections(R-Work) 4666
    R-Factor(R-Work) 0.1518
    R-Factor(R-Free) 0.1742
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2099
    Shell Resolution(Low) 2.2983
    Number of Reflections(Observed) 4945
    Number of Reflections(R-Free) 245
    Number of Reflections(R-Work) 4700
    R-Factor(R-Work) 0.1583
    R-Factor(R-Free) 0.1757
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2983
    Shell Resolution(Low) 2.4029
    Number of Reflections(Observed) 4952
    Number of Reflections(R-Free) 252
    Number of Reflections(R-Work) 4700
    R-Factor(R-Work) 0.1609
    R-Factor(R-Free) 0.1987
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4029
    Shell Resolution(Low) 2.5295
    Number of Reflections(Observed) 4923
    Number of Reflections(R-Free) 240
    Number of Reflections(R-Work) 4683
    R-Factor(R-Work) 0.161
    R-Factor(R-Free) 0.1897
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5295
    Shell Resolution(Low) 2.6879
    Number of Reflections(Observed) 4985
    Number of Reflections(R-Free) 249
    Number of Reflections(R-Work) 4736
    R-Factor(R-Work) 0.1731
    R-Factor(R-Free) 0.1934
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6879
    Shell Resolution(Low) 2.8953
    Number of Reflections(Observed) 4984
    Number of Reflections(R-Free) 247
    Number of Reflections(R-Work) 4737
    R-Factor(R-Work) 0.1692
    R-Factor(R-Free) 0.2075
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8953
    Shell Resolution(Low) 3.1864
    Number of Reflections(Observed) 4997
    Number of Reflections(R-Free) 254
    Number of Reflections(R-Work) 4743
    R-Factor(R-Work) 0.1651
    R-Factor(R-Free) 0.1868
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1864
    Shell Resolution(Low) 3.6469
    Number of Reflections(Observed) 5017
    Number of Reflections(R-Free) 250
    Number of Reflections(R-Work) 4767
    R-Factor(R-Work) 0.1427
    R-Factor(R-Free) 0.1366
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6469
    Shell Resolution(Low) 4.5923
    Number of Reflections(Observed) 5073
    Number of Reflections(R-Free) 250
    Number of Reflections(R-Work) 4823
    R-Factor(R-Work) 0.1292
    R-Factor(R-Free) 0.1386
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5923
    Shell Resolution(Low) 31.0047
    Number of Reflections(Observed) 5264
    Number of Reflections(R-Free) 268
    Number of Reflections(R-Work) 4996
    R-Factor(R-Work) 0.1602
    R-Factor(R-Free) 0.1622
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 14.857
    f_plane_restr 0.006
    f_chiral_restr 0.075
    f_angle_d 1.143
    f_bond_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 7764
    Nucleic Acid Atoms 0
    Heterogen Atoms 100
    Solvent Atoms 1326
     
     
  •   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: 1.7.3_928)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction HKL