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X-RAY DIFFRACTION
Materials and Methods page
3Q38
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.5
    Temperature 293.0
    Details 0.1 M Imidazole, 8.25% (w/v) PEG 8000, 1% (v/v) MPD, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.5
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 65.23 α = 90
    b = 79.03 β = 99.84
    c = 69.64 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 95
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 225 mm CCD
    Collection Date 2010-08-08
     
    Diffraction Radiation
    Monochromator Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 22-BM
    Wavelength List 1.0
    Site APS
    Beamline 22-BM
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.28
    Resolution(Low) 29.04
    Number Reflections(Observed) 178400
    Percent Possible(Observed) 99.8
    B(Isotropic) From Wilson Plot 12.1
    Redundancy 3.7
     
    High Resolution Shell Details
    Resolution(High) 1.28
    Resolution(Low) 1.31
    Percent Possible(All) 99.8
    Mean I Over Sigma(Observed) 2.14
    R-Sym I(Observed) 0.725
    Redundancy 3.6
    Number Unique Reflections(All) 13137
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.28
    Resolution(Low) 29.038
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 178400
    Number of Reflections(Observed) 178393
    Number of Reflections(R-Free) 8988
    Percent Reflections(Observed) 99.83
    R-Factor(Observed) 0.1675
    R-Work 0.1667
    R-Free 0.1814
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model Isotropic, TLS
    Mean Isotropic B Value 21.433
    Anisotropic B[1][1] -0.8882
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -1.8004
    Anisotropic B[2][2] -0.6755
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 1.5637
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.28
    Shell Resolution(Low) 1.2945
    Number of Reflections(Observed) 5537
    Number of Reflections(R-Free) 332
    Number of Reflections(R-Work) 5537
    R-Factor(R-Work) 0.2791
    R-Factor(R-Free) 0.2814
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.2945
    Shell Resolution(Low) 1.3098
    Number of Reflections(Observed) 5662
    Number of Reflections(R-Free) 278
    Number of Reflections(R-Work) 5662
    R-Factor(R-Work) 0.2603
    R-Factor(R-Free) 0.2613
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3098
    Shell Resolution(Low) 1.3257
    Number of Reflections(Observed) 5634
    Number of Reflections(R-Free) 287
    Number of Reflections(R-Work) 5634
    R-Factor(R-Work) 0.2565
    R-Factor(R-Free) 0.2767
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3257
    Shell Resolution(Low) 1.3425
    Number of Reflections(Observed) 5639
    Number of Reflections(R-Free) 292
    Number of Reflections(R-Work) 5639
    R-Factor(R-Work) 0.2479
    R-Factor(R-Free) 0.2825
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3425
    Shell Resolution(Low) 1.3602
    Number of Reflections(Observed) 5671
    Number of Reflections(R-Free) 279
    Number of Reflections(R-Work) 5671
    R-Factor(R-Work) 0.2423
    R-Factor(R-Free) 0.2331
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3602
    Shell Resolution(Low) 1.3788
    Number of Reflections(Observed) 5598
    Number of Reflections(R-Free) 301
    Number of Reflections(R-Work) 5598
    R-Factor(R-Work) 0.2281
    R-Factor(R-Free) 0.2522
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3788
    Shell Resolution(Low) 1.3985
    Number of Reflections(Observed) 5679
    Number of Reflections(R-Free) 280
    Number of Reflections(R-Work) 5679
    R-Factor(R-Work) 0.2173
    R-Factor(R-Free) 0.2232
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3985
    Shell Resolution(Low) 1.4194
    Number of Reflections(Observed) 5615
    Number of Reflections(R-Free) 316
    Number of Reflections(R-Work) 5615
    R-Factor(R-Work) 0.2119
    R-Factor(R-Free) 0.2262
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4194
    Shell Resolution(Low) 1.4416
    Number of Reflections(Observed) 5629
    Number of Reflections(R-Free) 303
    Number of Reflections(R-Work) 5629
    R-Factor(R-Work) 0.2058
    R-Factor(R-Free) 0.2413
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4416
    Shell Resolution(Low) 1.4652
    Number of Reflections(Observed) 5628
    Number of Reflections(R-Free) 308
    Number of Reflections(R-Work) 5628
    R-Factor(R-Work) 0.1908
    R-Factor(R-Free) 0.2171
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4652
    Shell Resolution(Low) 1.4905
    Number of Reflections(Observed) 5616
    Number of Reflections(R-Free) 314
    Number of Reflections(R-Work) 5616
    R-Factor(R-Work) 0.1895
    R-Factor(R-Free) 0.2028
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4905
    Shell Resolution(Low) 1.5176
    Number of Reflections(Observed) 5627
    Number of Reflections(R-Free) 319
    Number of Reflections(R-Work) 5627
    R-Factor(R-Work) 0.183
    R-Factor(R-Free) 0.1981
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5176
    Shell Resolution(Low) 1.5468
    Number of Reflections(Observed) 5646
    Number of Reflections(R-Free) 303
    Number of Reflections(R-Work) 5646
    R-Factor(R-Work) 0.1766
    R-Factor(R-Free) 0.2087
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5468
    Shell Resolution(Low) 1.5783
    Number of Reflections(Observed) 5621
    Number of Reflections(R-Free) 286
    Number of Reflections(R-Work) 5621
    R-Factor(R-Work) 0.1695
    R-Factor(R-Free) 0.1922
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5783
    Shell Resolution(Low) 1.6126
    Number of Reflections(Observed) 5646
    Number of Reflections(R-Free) 308
    Number of Reflections(R-Work) 5646
    R-Factor(R-Work) 0.1624
    R-Factor(R-Free) 0.1867
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6126
    Shell Resolution(Low) 1.6502
    Number of Reflections(Observed) 5644
    Number of Reflections(R-Free) 307
    Number of Reflections(R-Work) 5644
    R-Factor(R-Work) 0.1644
    R-Factor(R-Free) 0.1972
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6502
    Shell Resolution(Low) 1.6914
    Number of Reflections(Observed) 5603
    Number of Reflections(R-Free) 322
    Number of Reflections(R-Work) 5603
    R-Factor(R-Work) 0.1597
    R-Factor(R-Free) 0.1727
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6914
    Shell Resolution(Low) 1.7371
    Number of Reflections(Observed) 5692
    Number of Reflections(R-Free) 272
    Number of Reflections(R-Work) 5692
    R-Factor(R-Work) 0.1544
    R-Factor(R-Free) 0.174
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7371
    Shell Resolution(Low) 1.7883
    Number of Reflections(Observed) 5632
    Number of Reflections(R-Free) 296
    Number of Reflections(R-Work) 5632
    R-Factor(R-Work) 0.1485
    R-Factor(R-Free) 0.166
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7883
    Shell Resolution(Low) 1.846
    Number of Reflections(Observed) 5643
    Number of Reflections(R-Free) 302
    Number of Reflections(R-Work) 5643
    R-Factor(R-Work) 0.1409
    R-Factor(R-Free) 0.1563
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.846
    Shell Resolution(Low) 1.9119
    Number of Reflections(Observed) 5640
    Number of Reflections(R-Free) 303
    Number of Reflections(R-Work) 5640
    R-Factor(R-Work) 0.1489
    R-Factor(R-Free) 0.1591
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9119
    Shell Resolution(Low) 1.9885
    Number of Reflections(Observed) 5675
    Number of Reflections(R-Free) 320
    Number of Reflections(R-Work) 5675
    R-Factor(R-Work) 0.1481
    R-Factor(R-Free) 0.1619
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9885
    Shell Resolution(Low) 2.0789
    Number of Reflections(Observed) 5637
    Number of Reflections(R-Free) 280
    Number of Reflections(R-Work) 5637
    R-Factor(R-Work) 0.1479
    R-Factor(R-Free) 0.1539
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0789
    Shell Resolution(Low) 2.1885
    Number of Reflections(Observed) 5666
    Number of Reflections(R-Free) 284
    Number of Reflections(R-Work) 5666
    R-Factor(R-Work) 0.1521
    R-Factor(R-Free) 0.1581
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1885
    Shell Resolution(Low) 2.3256
    Number of Reflections(Observed) 5671
    Number of Reflections(R-Free) 321
    Number of Reflections(R-Work) 5671
    R-Factor(R-Work) 0.1552
    R-Factor(R-Free) 0.1606
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3256
    Shell Resolution(Low) 2.505
    Number of Reflections(Observed) 5642
    Number of Reflections(R-Free) 317
    Number of Reflections(R-Work) 5642
    R-Factor(R-Work) 0.1552
    R-Factor(R-Free) 0.1706
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.505
    Shell Resolution(Low) 2.757
    Number of Reflections(Observed) 5658
    Number of Reflections(R-Free) 287
    Number of Reflections(R-Work) 5658
    R-Factor(R-Work) 0.1642
    R-Factor(R-Free) 0.1784
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.757
    Shell Resolution(Low) 3.1555
    Number of Reflections(Observed) 5698
    Number of Reflections(R-Free) 286
    Number of Reflections(R-Work) 5698
    R-Factor(R-Work) 0.1701
    R-Factor(R-Free) 0.1864
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1555
    Shell Resolution(Low) 3.974
    Number of Reflections(Observed) 5692
    Number of Reflections(R-Free) 296
    Number of Reflections(R-Work) 5692
    R-Factor(R-Work) 0.1569
    R-Factor(R-Free) 0.1783
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.974
    Shell Resolution(Low) 29.0453
    Number of Reflections(Observed) 5764
    Number of Reflections(R-Free) 289
    Number of Reflections(R-Work) 5764
    R-Factor(R-Work) 0.1533
    R-Factor(R-Free) 0.1625
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.008
    f_chiral_restr 0.095
    f_dihedral_angle_d 13.683
    f_angle_d 1.357
    f_bond_d 0.011
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4829
    Nucleic Acid Atoms 0
    Heterogen Atoms 139
    Solvent Atoms 825
     
     
  •   Software and Computing Hide
    Computing
    Data Collection SERGUI
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution PHASER (2.1.4)
    Structure Refinement PHENIX (phenix.refine: 1.6.4_486)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.6.4_486)
    model building PHASER version: (2.1.4)
    data collection SERGUI