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X-RAY DIFFRACTION
Materials and Methods page
4DQ5
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion, hanging drop
    pH 6.5
    Temperature 289.0
    Details 1.6 M Na-Acetate, 0.1 M Na-Citrate, pH 6.5, vapor diffusion, hanging drop, temperature 289K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 62.16 α = 90
    b = 68.79 β = 90
    c = 90.04 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Collection Date 2011-01-01
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X29A
    Wavelength List 1.075
    Site NSLS
    Beamline X29A
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 1.39
    Resolution(Low) 60
    Number Reflections(Observed) 77074
    Percent Possible(Observed) 99.8
    R Merge I(Observed) 0.058
    Redundancy 4.9
     
    High Resolution Shell Details
    Resolution(High) 1.395
    Resolution(Low) 1.42
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.638
    Redundancy 4.1
    Number Unique Reflections(All) 3829
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method SAD
    reflnsShellList 1.395
    Resolution(Low) 37.67
    Cut-off Sigma(F) 1.36
    Number of Reflections(all) 77074
    Number of Reflections(Observed) 77006
    Number of Reflections(R-Free) 7698
    Percent Reflections(Observed) 99.47
    R-Factor(Observed) 0.1657
    R-Work 0.1645
    R-Free 0.1773
     
    Temperature Factor Modeling
    Mean Isotropic B Value 25.4023
    Anisotropic B[1][1] 0.657
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 1.1565
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -1.8135
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.395
    Shell Resolution(Low) 1.4113
    Number of Reflections(R-Free) 226
    Number of Reflections(R-Work) 2049
    R-Factor(R-Work) 0.3158
    R-Factor(R-Free) 0.3285
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4113
    Shell Resolution(Low) 1.4279
    Number of Reflections(R-Free) 254
    Number of Reflections(R-Work) 2280
    R-Factor(R-Work) 0.3024
    R-Factor(R-Free) 0.3231
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4279
    Shell Resolution(Low) 1.4453
    Number of Reflections(R-Free) 255
    Number of Reflections(R-Work) 2306
    R-Factor(R-Work) 0.2745
    R-Factor(R-Free) 0.2844
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4453
    Shell Resolution(Low) 1.4636
    Number of Reflections(R-Free) 254
    Number of Reflections(R-Work) 2275
    R-Factor(R-Work) 0.2464
    R-Factor(R-Free) 0.2708
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4636
    Shell Resolution(Low) 1.4828
    Number of Reflections(R-Free) 256
    Number of Reflections(R-Work) 2306
    R-Factor(R-Work) 0.2297
    R-Factor(R-Free) 0.2608
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4828
    Shell Resolution(Low) 1.5031
    Number of Reflections(R-Free) 256
    Number of Reflections(R-Work) 2302
    R-Factor(R-Work) 0.2167
    R-Factor(R-Free) 0.2381
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5031
    Shell Resolution(Low) 1.5246
    Number of Reflections(R-Free) 255
    Number of Reflections(R-Work) 2299
    R-Factor(R-Work) 0.2082
    R-Factor(R-Free) 0.2306
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5246
    Shell Resolution(Low) 1.5474
    Number of Reflections(R-Free) 254
    Number of Reflections(R-Work) 2280
    R-Factor(R-Work) 0.1911
    R-Factor(R-Free) 0.2113
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5474
    Shell Resolution(Low) 1.5715
    Number of Reflections(R-Free) 255
    Number of Reflections(R-Work) 2297
    R-Factor(R-Work) 0.1822
    R-Factor(R-Free) 0.2154
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5715
    Shell Resolution(Low) 1.5973
    Number of Reflections(R-Free) 258
    Number of Reflections(R-Work) 2323
    R-Factor(R-Work) 0.177
    R-Factor(R-Free) 0.2007
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5973
    Shell Resolution(Low) 1.6249
    Number of Reflections(R-Free) 253
    Number of Reflections(R-Work) 2268
    R-Factor(R-Work) 0.1685
    R-Factor(R-Free) 0.1907
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6249
    Shell Resolution(Low) 1.6544
    Number of Reflections(R-Free) 255
    Number of Reflections(R-Work) 2298
    R-Factor(R-Work) 0.1569
    R-Factor(R-Free) 0.1827
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6544
    Shell Resolution(Low) 1.6862
    Number of Reflections(R-Free) 258
    Number of Reflections(R-Work) 2323
    R-Factor(R-Work) 0.1606
    R-Factor(R-Free) 0.1924
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6862
    Shell Resolution(Low) 1.7206
    Number of Reflections(R-Free) 257
    Number of Reflections(R-Work) 2310
    R-Factor(R-Work) 0.1549
    R-Factor(R-Free) 0.1761
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7206
    Shell Resolution(Low) 1.7581
    Number of Reflections(R-Free) 253
    Number of Reflections(R-Work) 2279
    R-Factor(R-Work) 0.1565
    R-Factor(R-Free) 0.1791
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7581
    Shell Resolution(Low) 1.799
    Number of Reflections(R-Free) 258
    Number of Reflections(R-Work) 2322
    R-Factor(R-Work) 0.1595
    R-Factor(R-Free) 0.1724
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.799
    Shell Resolution(Low) 1.8439
    Number of Reflections(R-Free) 255
    Number of Reflections(R-Work) 2294
    R-Factor(R-Work) 0.1588
    R-Factor(R-Free) 0.1738
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8439
    Shell Resolution(Low) 1.8938
    Number of Reflections(R-Free) 259
    Number of Reflections(R-Work) 2334
    R-Factor(R-Work) 0.1607
    R-Factor(R-Free) 0.183
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8938
    Shell Resolution(Low) 1.9495
    Number of Reflections(R-Free) 256
    Number of Reflections(R-Work) 2300
    R-Factor(R-Work) 0.1569
    R-Factor(R-Free) 0.1821
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9495
    Shell Resolution(Low) 2.0124
    Number of Reflections(R-Free) 255
    Number of Reflections(R-Work) 2298
    R-Factor(R-Work) 0.1561
    R-Factor(R-Free) 0.1678
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0124
    Shell Resolution(Low) 2.0844
    Number of Reflections(R-Free) 260
    Number of Reflections(R-Work) 2336
    R-Factor(R-Work) 0.1591
    R-Factor(R-Free) 0.1718
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0844
    Shell Resolution(Low) 2.1678
    Number of Reflections(R-Free) 256
    Number of Reflections(R-Work) 2306
    R-Factor(R-Work) 0.1556
    R-Factor(R-Free) 0.1791
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1678
    Shell Resolution(Low) 2.2665
    Number of Reflections(R-Free) 260
    Number of Reflections(R-Work) 2344
    R-Factor(R-Work) 0.1483
    R-Factor(R-Free) 0.153
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2665
    Shell Resolution(Low) 2.3859
    Number of Reflections(R-Free) 259
    Number of Reflections(R-Work) 2333
    R-Factor(R-Work) 0.1414
    R-Factor(R-Free) 0.1575
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3859
    Shell Resolution(Low) 2.5354
    Number of Reflections(R-Free) 258
    Number of Reflections(R-Work) 2326
    R-Factor(R-Work) 0.1479
    R-Factor(R-Free) 0.166
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5354
    Shell Resolution(Low) 2.7311
    Number of Reflections(R-Free) 263
    Number of Reflections(R-Work) 2361
    R-Factor(R-Work) 0.158
    R-Factor(R-Free) 0.1729
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7311
    Shell Resolution(Low) 3.0058
    Number of Reflections(R-Free) 262
    Number of Reflections(R-Work) 2354
    R-Factor(R-Work) 0.1672
    R-Factor(R-Free) 0.1872
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0058
    Shell Resolution(Low) 3.4405
    Number of Reflections(R-Free) 263
    Number of Reflections(R-Work) 2375
    R-Factor(R-Work) 0.1636
    R-Factor(R-Free) 0.1714
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4405
    Shell Resolution(Low) 4.3337
    Number of Reflections(R-Free) 264
    Number of Reflections(R-Work) 2385
    R-Factor(R-Work) 0.1489
    R-Factor(R-Free) 0.1474
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3337
    Shell Resolution(Low) 37.67
    Number of Reflections(R-Free) 271
    Number of Reflections(R-Work) 2445
    R-Factor(R-Work) 0.1754
    R-Factor(R-Free) 0.1832
    Percent Reflections(Observed) 97.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 14.406
    f_plane_restr 0.005
    f_chiral_restr 0.056
    f_angle_d 1.017
    f_bond_d 0.005
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2541
    Nucleic Acid Atoms 0
    Heterogen Atoms 26
    Solvent Atoms 479
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) SCALEPACK
    Structure Solution HKL2MAP
    Structure Refinement PHENIX (phenix.refine: 1.7.3_928)
     
    Software
    data extraction pdb_extract version: 3.10
    refinement phenix
    data reduction SCALEPACK