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X-RAY DIFFRACTION
Materials and Methods page
4GKK
  •   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 = 402.37 α = 90
    b = 402.37 β = 90
    c = 175.62 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 2010-08-11
     
    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) 3.2
    Resolution(Low) 73.5
    Number Reflections(Observed) 230910
    Percent Possible(Observed) 47.9
     
    High Resolution Shell Details
    Resolution(High) 2.91
    Resolution(Low) 3.05
    Percent Possible(All) 78.6
    R Merge I(Observed) 0.017
    Mean I Over Sigma(Observed) 0.15
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 3.2
    Resolution(Low) 73.466
    Cut-off Sigma(F) 0.78
    Number of Reflections(Observed) 230816
    Number of Reflections(R-Free) 11785
    Percent Reflections(Observed) 98.3
    R-Factor(Observed) 0.1973
    R-Work 0.1952
    R-Free 0.2359
     
    Temperature Factor Modeling
    Mean Isotropic B Value 96.1629
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2
    Shell Resolution(Low) 3.2364
    Number of Reflections(R-Free) 370
    Number of Reflections(R-Work) 7262
    R-Factor(R-Work) 0.3296
    R-Factor(R-Free) 0.3571
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2364
    Shell Resolution(Low) 3.2744
    Number of Reflections(R-Free) 380
    Number of Reflections(R-Work) 7315
    R-Factor(R-Work) 0.3183
    R-Factor(R-Free) 0.343
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2744
    Shell Resolution(Low) 3.3144
    Number of Reflections(R-Free) 376
    Number of Reflections(R-Work) 7312
    R-Factor(R-Work) 0.3018
    R-Factor(R-Free) 0.3474
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3144
    Shell Resolution(Low) 3.3563
    Number of Reflections(R-Free) 371
    Number of Reflections(R-Work) 7325
    R-Factor(R-Work) 0.2956
    R-Factor(R-Free) 0.3261
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3563
    Shell Resolution(Low) 3.4005
    Number of Reflections(R-Free) 382
    Number of Reflections(R-Work) 7323
    R-Factor(R-Work) 0.2838
    R-Factor(R-Free) 0.3155
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4005
    Shell Resolution(Low) 3.4471
    Number of Reflections(R-Free) 418
    Number of Reflections(R-Work) 7319
    R-Factor(R-Work) 0.2672
    R-Factor(R-Free) 0.3014
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4471
    Shell Resolution(Low) 3.4963
    Number of Reflections(R-Free) 412
    Number of Reflections(R-Work) 7249
    R-Factor(R-Work) 0.2611
    R-Factor(R-Free) 0.2973
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4963
    Shell Resolution(Low) 3.5485
    Number of Reflections(R-Free) 430
    Number of Reflections(R-Work) 7250
    R-Factor(R-Work) 0.2565
    R-Factor(R-Free) 0.292
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5485
    Shell Resolution(Low) 3.604
    Number of Reflections(R-Free) 412
    Number of Reflections(R-Work) 7325
    R-Factor(R-Work) 0.2377
    R-Factor(R-Free) 0.2847
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.604
    Shell Resolution(Low) 3.663
    Number of Reflections(R-Free) 395
    Number of Reflections(R-Work) 7331
    R-Factor(R-Work) 0.2264
    R-Factor(R-Free) 0.2684
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.663
    Shell Resolution(Low) 3.7262
    Number of Reflections(R-Free) 434
    Number of Reflections(R-Work) 7262
    R-Factor(R-Work) 0.2207
    R-Factor(R-Free) 0.2496
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7262
    Shell Resolution(Low) 3.7939
    Number of Reflections(R-Free) 406
    Number of Reflections(R-Work) 7276
    R-Factor(R-Work) 0.1993
    R-Factor(R-Free) 0.2506
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7939
    Shell Resolution(Low) 3.8669
    Number of Reflections(R-Free) 382
    Number of Reflections(R-Work) 7327
    R-Factor(R-Work) 0.1901
    R-Factor(R-Free) 0.2212
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8669
    Shell Resolution(Low) 3.9458
    Number of Reflections(R-Free) 419
    Number of Reflections(R-Work) 7264
    R-Factor(R-Work) 0.1827
    R-Factor(R-Free) 0.2324
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9458
    Shell Resolution(Low) 4.0316
    Number of Reflections(R-Free) 388
    Number of Reflections(R-Work) 7334
    R-Factor(R-Work) 0.1788
    R-Factor(R-Free) 0.2207
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0316
    Shell Resolution(Low) 4.1254
    Number of Reflections(R-Free) 385
    Number of Reflections(R-Work) 7341
    R-Factor(R-Work) 0.18
    R-Factor(R-Free) 0.2257
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1254
    Shell Resolution(Low) 4.2286
    Number of Reflections(R-Free) 418
    Number of Reflections(R-Work) 7291
    R-Factor(R-Work) 0.1729
    R-Factor(R-Free) 0.2101
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2286
    Shell Resolution(Low) 4.3429
    Number of Reflections(R-Free) 372
    Number of Reflections(R-Work) 7363
    R-Factor(R-Work) 0.1625
    R-Factor(R-Free) 0.2064
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3429
    Shell Resolution(Low) 4.4707
    Number of Reflections(R-Free) 391
    Number of Reflections(R-Work) 7350
    R-Factor(R-Work) 0.164
    R-Factor(R-Free) 0.214
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4707
    Shell Resolution(Low) 4.6149
    Number of Reflections(R-Free) 391
    Number of Reflections(R-Work) 7327
    R-Factor(R-Work) 0.1617
    R-Factor(R-Free) 0.203
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6149
    Shell Resolution(Low) 4.7799
    Number of Reflections(R-Free) 393
    Number of Reflections(R-Work) 7338
    R-Factor(R-Work) 0.1624
    R-Factor(R-Free) 0.1911
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7799
    Shell Resolution(Low) 4.9712
    Number of Reflections(R-Free) 376
    Number of Reflections(R-Work) 7357
    R-Factor(R-Work) 0.1612
    R-Factor(R-Free) 0.21
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9712
    Shell Resolution(Low) 5.1974
    Number of Reflections(R-Free) 378
    Number of Reflections(R-Work) 7358
    R-Factor(R-Work) 0.1573
    R-Factor(R-Free) 0.1971
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1974
    Shell Resolution(Low) 5.4713
    Number of Reflections(R-Free) 415
    Number of Reflections(R-Work) 7331
    R-Factor(R-Work) 0.1528
    R-Factor(R-Free) 0.2077
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.4713
    Shell Resolution(Low) 5.814
    Number of Reflections(R-Free) 388
    Number of Reflections(R-Work) 7344
    R-Factor(R-Work) 0.1576
    R-Factor(R-Free) 0.2242
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.814
    Shell Resolution(Low) 6.2627
    Number of Reflections(R-Free) 347
    Number of Reflections(R-Work) 7360
    R-Factor(R-Work) 0.1637
    R-Factor(R-Free) 0.2065
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.2627
    Shell Resolution(Low) 6.8925
    Number of Reflections(R-Free) 412
    Number of Reflections(R-Work) 7281
    R-Factor(R-Work) 0.1639
    R-Factor(R-Free) 0.2155
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.8925
    Shell Resolution(Low) 7.8888
    Number of Reflections(R-Free) 372
    Number of Reflections(R-Work) 7294
    R-Factor(R-Work) 0.1596
    R-Factor(R-Free) 0.2034
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.8888
    Shell Resolution(Low) 9.9352
    Number of Reflections(R-Free) 397
    Number of Reflections(R-Work) 7219
    R-Factor(R-Work) 0.1815
    R-Factor(R-Free) 0.2225
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 9.9352
    Shell Resolution(Low) 73.485
    Number of Reflections(R-Free) 375
    Number of Reflections(R-Work) 7003
    R-Factor(R-Work) 0.2519
    R-Factor(R-Free) 0.2672
    Percent Reflections(Observed) 88.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.006
    f_chiral_restr 0.068
    f_dihedral_angle_d 18.427
    f_angle_d 1.347
    f_bond_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 19231
    Nucleic Acid Atoms 32727
    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