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X-RAY DIFFRACTION
Materials and Methods page
4GKJ
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.5
    Temperature 277.0
    Details MPD, NH4Cl, KCl, CaCl2, magnesium acetate, sodium cacodylate, pH 6.5 VAPOR DIFFUSION, HANGING DROP, temperature 277K, temperature 277.0K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 400.55 α = 90
    b = 400.55 β = 90
    c = 176.19 γ = 90
     
    Space Group
    Space Group Name:    P 41 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2010-08-17
     
    Diffraction Radiation
    Monochromator Silicon
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 24-ID-C
    Wavelength List 0.97
    Site APS
    Beamline 24-ID-C
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 3
    Resolution(Low) 283
    Number Reflections(Observed) 276947
    Percent Possible(Observed) 62.3
     
    High Resolution Shell Details
    Resolution(High) 2.9
    Resolution(Low) 3.04
    Percent Possible(All) 98.1
    R Merge I(Observed) 9.636
    Mean I Over Sigma(Observed) 0.21
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 3.298
    Resolution(Low) 97.148
    Cut-off Sigma(F) 0.92
    Number of Reflections(Observed) 207838
    Number of Reflections(R-Free) 10445
    Percent Reflections(Observed) 97.34
    R-Factor(Observed) 0.19
    R-Work 0.1884
    R-Free 0.2216
     
    Temperature Factor Modeling
    Mean Isotropic B Value 92.8082
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.298
    Shell Resolution(Low) 3.3355
    Number of Reflections(R-Free) 305
    Number of Reflections(R-Work) 6022
    R-Factor(R-Work) 0.3227
    R-Factor(R-Free) 0.3387
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3355
    Shell Resolution(Low) 3.3747
    Number of Reflections(R-Free) 369
    Number of Reflections(R-Work) 6620
    R-Factor(R-Work) 0.2941
    R-Factor(R-Free) 0.3308
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3747
    Shell Resolution(Low) 3.4159
    Number of Reflections(R-Free) 343
    Number of Reflections(R-Work) 6675
    R-Factor(R-Work) 0.2781
    R-Factor(R-Free) 0.2985
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4159
    Shell Resolution(Low) 3.4591
    Number of Reflections(R-Free) 344
    Number of Reflections(R-Work) 6699
    R-Factor(R-Work) 0.2701
    R-Factor(R-Free) 0.3002
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4591
    Shell Resolution(Low) 3.5047
    Number of Reflections(R-Free) 374
    Number of Reflections(R-Work) 6632
    R-Factor(R-Work) 0.2645
    R-Factor(R-Free) 0.3024
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5047
    Shell Resolution(Low) 3.5527
    Number of Reflections(R-Free) 348
    Number of Reflections(R-Work) 6704
    R-Factor(R-Work) 0.2487
    R-Factor(R-Free) 0.2832
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5527
    Shell Resolution(Low) 3.6034
    Number of Reflections(R-Free) 351
    Number of Reflections(R-Work) 6691
    R-Factor(R-Work) 0.2353
    R-Factor(R-Free) 0.2581
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6034
    Shell Resolution(Low) 3.6572
    Number of Reflections(R-Free) 360
    Number of Reflections(R-Work) 6652
    R-Factor(R-Work) 0.2232
    R-Factor(R-Free) 0.2448
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6572
    Shell Resolution(Low) 3.7144
    Number of Reflections(R-Free) 331
    Number of Reflections(R-Work) 6682
    R-Factor(R-Work) 0.2183
    R-Factor(R-Free) 0.2492
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7144
    Shell Resolution(Low) 3.7753
    Number of Reflections(R-Free) 345
    Number of Reflections(R-Work) 6667
    R-Factor(R-Work) 0.2059
    R-Factor(R-Free) 0.2357
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7753
    Shell Resolution(Low) 3.8404
    Number of Reflections(R-Free) 335
    Number of Reflections(R-Work) 6691
    R-Factor(R-Work) 0.2006
    R-Factor(R-Free) 0.2299
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8404
    Shell Resolution(Low) 3.9102
    Number of Reflections(R-Free) 381
    Number of Reflections(R-Work) 6622
    R-Factor(R-Work) 0.1923
    R-Factor(R-Free) 0.2318
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9102
    Shell Resolution(Low) 3.9854
    Number of Reflections(R-Free) 338
    Number of Reflections(R-Work) 6671
    R-Factor(R-Work) 0.1834
    R-Factor(R-Free) 0.2311
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9854
    Shell Resolution(Low) 4.0668
    Number of Reflections(R-Free) 401
    Number of Reflections(R-Work) 6594
    R-Factor(R-Work) 0.1809
    R-Factor(R-Free) 0.2301
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0668
    Shell Resolution(Low) 4.1552
    Number of Reflections(R-Free) 348
    Number of Reflections(R-Work) 6639
    R-Factor(R-Work) 0.1685
    R-Factor(R-Free) 0.2086
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1552
    Shell Resolution(Low) 4.2519
    Number of Reflections(R-Free) 369
    Number of Reflections(R-Work) 6666
    R-Factor(R-Work) 0.1668
    R-Factor(R-Free) 0.2161
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2519
    Shell Resolution(Low) 4.3582
    Number of Reflections(R-Free) 335
    Number of Reflections(R-Work) 6668
    R-Factor(R-Work) 0.1712
    R-Factor(R-Free) 0.2035
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3582
    Shell Resolution(Low) 4.476
    Number of Reflections(R-Free) 373
    Number of Reflections(R-Work) 6641
    R-Factor(R-Work) 0.1669
    R-Factor(R-Free) 0.2021
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.476
    Shell Resolution(Low) 4.6077
    Number of Reflections(R-Free) 307
    Number of Reflections(R-Work) 6687
    R-Factor(R-Work) 0.1619
    R-Factor(R-Free) 0.2013
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6077
    Shell Resolution(Low) 4.7564
    Number of Reflections(R-Free) 356
    Number of Reflections(R-Work) 6645
    R-Factor(R-Work) 0.1578
    R-Factor(R-Free) 0.1814
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7564
    Shell Resolution(Low) 4.9264
    Number of Reflections(R-Free) 338
    Number of Reflections(R-Work) 6612
    R-Factor(R-Work) 0.1527
    R-Factor(R-Free) 0.1898
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9264
    Shell Resolution(Low) 5.1237
    Number of Reflections(R-Free) 380
    Number of Reflections(R-Work) 6593
    R-Factor(R-Work) 0.15
    R-Factor(R-Free) 0.1928
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1237
    Shell Resolution(Low) 5.3568
    Number of Reflections(R-Free) 351
    Number of Reflections(R-Work) 6617
    R-Factor(R-Work) 0.1435
    R-Factor(R-Free) 0.1909
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.3568
    Shell Resolution(Low) 5.6392
    Number of Reflections(R-Free) 337
    Number of Reflections(R-Work) 6597
    R-Factor(R-Work) 0.1471
    R-Factor(R-Free) 0.1945
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.6392
    Shell Resolution(Low) 5.9925
    Number of Reflections(R-Free) 362
    Number of Reflections(R-Work) 6584
    R-Factor(R-Work) 0.1503
    R-Factor(R-Free) 0.2007
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.9925
    Shell Resolution(Low) 6.4551
    Number of Reflections(R-Free) 344
    Number of Reflections(R-Work) 6550
    R-Factor(R-Work) 0.1584
    R-Factor(R-Free) 0.2061
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.4551
    Shell Resolution(Low) 7.1045
    Number of Reflections(R-Free) 341
    Number of Reflections(R-Work) 6491
    R-Factor(R-Work) 0.1562
    R-Factor(R-Free) 0.1962
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.1045
    Shell Resolution(Low) 8.1321
    Number of Reflections(R-Free) 349
    Number of Reflections(R-Work) 6414
    R-Factor(R-Work) 0.1555
    R-Factor(R-Free) 0.1869
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.1321
    Shell Resolution(Low) 10.2439
    Number of Reflections(R-Free) 330
    Number of Reflections(R-Work) 6315
    R-Factor(R-Work) 0.1843
    R-Factor(R-Free) 0.2206
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 10.2439
    Shell Resolution(Low) 97.1898
    Number of Reflections(R-Free) 300
    Number of Reflections(R-Work) 6052
    R-Factor(R-Work) 0.2574
    R-Factor(R-Free) 0.2506
    Percent Reflections(Observed) 83.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.006
    f_chiral_restr 0.069
    f_dihedral_angle_d 18.343
    f_angle_d 1.354
    f_bond_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 19231
    Nucleic Acid Atoms 32766
    Heterogen Atoms 230
    Solvent Atoms 0
     
     
  •   Software and Computing Hide
    Computing
    Data Collection Console
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution PHENIX
    Structure Refinement PHENIX (phenix.refine: 1.8_1069)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction Xscale