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X-RAY DIFFRACTION
Materials and Methods page
4DR2
  •   Crystallization Hide
    Crystallization Experiments
    Method HANGING DROP
    pH 6.5
    Temperature 277.0
    Details MPD, pH 6.5, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 402.6 α = 90
    b = 402.6 β = 90
    c = 177.58 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 2008-10-14
     
    Diffraction Radiation
    Monochromator Kohzu HLD8-24
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 24-ID-C
    Wavelength List 0.98
    Site APS
    Beamline 24-ID-C
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) -3.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 3.25
    Resolution(Low) 45
    Number Reflections(All) 226409
    Number Reflections(Observed) 226409
    Percent Possible(Observed) 99.6
    R Merge I(Observed) 0.115
    Redundancy 3.7
     
    High Resolution Shell Details
    Resolution(High) 3.249
    Resolution(Low) 3.37
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.811
    Redundancy 3.8
    Number Unique Reflections(All) 22444
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 3.249
    Resolution(Low) 44.389
    Cut-off Sigma(F) 1.34
    Number of Reflections(all) 226222
    Number of Reflections(Observed) 226222
    Number of Reflections(R-Free) 11411
    Percent Reflections(Observed) 99.61
    R-Factor(Observed) 0.1731
    R-Work 0.1711
    R-Free 0.2109
    R-Free Selection Details FROM PDB ENTRY 2VQE
     
    Temperature Factor Modeling
    Mean Isotropic B Value 98.2273
    Anisotropic B[1][1] -8.6416
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -8.6416
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 17.2833
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.249
    Shell Resolution(Low) 3.2859
    Number of Reflections(R-Free) 394
    Number of Reflections(R-Work) 7113
    R-Factor(R-Work) 0.2983
    R-Factor(R-Free) 0.3553
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2859
    Shell Resolution(Low) 3.3246
    Number of Reflections(R-Free) 372
    Number of Reflections(R-Work) 7088
    R-Factor(R-Work) 0.2718
    R-Factor(R-Free) 0.2833
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3246
    Shell Resolution(Low) 3.3651
    Number of Reflections(R-Free) 398
    Number of Reflections(R-Work) 7084
    R-Factor(R-Work) 0.2573
    R-Factor(R-Free) 0.2946
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3651
    Shell Resolution(Low) 3.4077
    Number of Reflections(R-Free) 376
    Number of Reflections(R-Work) 7167
    R-Factor(R-Work) 0.2491
    R-Factor(R-Free) 0.2899
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4077
    Shell Resolution(Low) 3.4525
    Number of Reflections(R-Free) 380
    Number of Reflections(R-Work) 7053
    R-Factor(R-Work) 0.2418
    R-Factor(R-Free) 0.2669
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4525
    Shell Resolution(Low) 3.4998
    Number of Reflections(R-Free) 406
    Number of Reflections(R-Work) 7117
    R-Factor(R-Work) 0.2389
    R-Factor(R-Free) 0.2795
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4998
    Shell Resolution(Low) 3.5498
    Number of Reflections(R-Free) 393
    Number of Reflections(R-Work) 7160
    R-Factor(R-Work) 0.2169
    R-Factor(R-Free) 0.2552
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5498
    Shell Resolution(Low) 3.6027
    Number of Reflections(R-Free) 400
    Number of Reflections(R-Work) 7067
    R-Factor(R-Work) 0.2103
    R-Factor(R-Free) 0.2602
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6027
    Shell Resolution(Low) 3.659
    Number of Reflections(R-Free) 366
    Number of Reflections(R-Work) 7122
    R-Factor(R-Work) 0.2037
    R-Factor(R-Free) 0.2435
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.659
    Shell Resolution(Low) 3.719
    Number of Reflections(R-Free) 405
    Number of Reflections(R-Work) 7092
    R-Factor(R-Work) 0.1941
    R-Factor(R-Free) 0.2235
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.719
    Shell Resolution(Low) 3.783
    Number of Reflections(R-Free) 395
    Number of Reflections(R-Work) 7144
    R-Factor(R-Work) 0.1842
    R-Factor(R-Free) 0.2351
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.783
    Shell Resolution(Low) 3.8518
    Number of Reflections(R-Free) 345
    Number of Reflections(R-Work) 7174
    R-Factor(R-Work) 0.1826
    R-Factor(R-Free) 0.2175
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8518
    Shell Resolution(Low) 3.9258
    Number of Reflections(R-Free) 380
    Number of Reflections(R-Work) 7133
    R-Factor(R-Work) 0.1763
    R-Factor(R-Free) 0.2352
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9258
    Shell Resolution(Low) 4.0059
    Number of Reflections(R-Free) 361
    Number of Reflections(R-Work) 7162
    R-Factor(R-Work) 0.1722
    R-Factor(R-Free) 0.1973
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0059
    Shell Resolution(Low) 4.093
    Number of Reflections(R-Free) 413
    Number of Reflections(R-Work) 7109
    R-Factor(R-Work) 0.1613
    R-Factor(R-Free) 0.2061
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.093
    Shell Resolution(Low) 4.1881
    Number of Reflections(R-Free) 356
    Number of Reflections(R-Work) 7188
    R-Factor(R-Work) 0.1514
    R-Factor(R-Free) 0.1828
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1881
    Shell Resolution(Low) 4.2928
    Number of Reflections(R-Free) 379
    Number of Reflections(R-Work) 7140
    R-Factor(R-Work) 0.1476
    R-Factor(R-Free) 0.1981
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2928
    Shell Resolution(Low) 4.4087
    Number of Reflections(R-Free) 405
    Number of Reflections(R-Work) 7142
    R-Factor(R-Work) 0.1452
    R-Factor(R-Free) 0.1846
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4087
    Shell Resolution(Low) 4.5383
    Number of Reflections(R-Free) 397
    Number of Reflections(R-Work) 7172
    R-Factor(R-Work) 0.1437
    R-Factor(R-Free) 0.1768
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5383
    Shell Resolution(Low) 4.6847
    Number of Reflections(R-Free) 355
    Number of Reflections(R-Work) 7204
    R-Factor(R-Work) 0.1452
    R-Factor(R-Free) 0.2028
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6847
    Shell Resolution(Low) 4.8519
    Number of Reflections(R-Free) 344
    Number of Reflections(R-Work) 7188
    R-Factor(R-Work) 0.1412
    R-Factor(R-Free) 0.1944
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8519
    Shell Resolution(Low) 5.0459
    Number of Reflections(R-Free) 393
    Number of Reflections(R-Work) 7160
    R-Factor(R-Work) 0.1363
    R-Factor(R-Free) 0.1813
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0459
    Shell Resolution(Low) 5.2752
    Number of Reflections(R-Free) 362
    Number of Reflections(R-Work) 7211
    R-Factor(R-Work) 0.1381
    R-Factor(R-Free) 0.1783
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2752
    Shell Resolution(Low) 5.5528
    Number of Reflections(R-Free) 380
    Number of Reflections(R-Work) 7210
    R-Factor(R-Work) 0.1355
    R-Factor(R-Free) 0.1861
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.5528
    Shell Resolution(Low) 5.9
    Number of Reflections(R-Free) 385
    Number of Reflections(R-Work) 7235
    R-Factor(R-Work) 0.135
    R-Factor(R-Free) 0.1772
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.9
    Shell Resolution(Low) 6.3543
    Number of Reflections(R-Free) 347
    Number of Reflections(R-Work) 7249
    R-Factor(R-Work) 0.1394
    R-Factor(R-Free) 0.1894
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.3543
    Shell Resolution(Low) 6.9916
    Number of Reflections(R-Free) 375
    Number of Reflections(R-Work) 7231
    R-Factor(R-Work) 0.1378
    R-Factor(R-Free) 0.1849
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.9916
    Shell Resolution(Low) 7.9982
    Number of Reflections(R-Free) 368
    Number of Reflections(R-Work) 7245
    R-Factor(R-Work) 0.1401
    R-Factor(R-Free) 0.1814
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.9982
    Shell Resolution(Low) 10.0575
    Number of Reflections(R-Free) 399
    Number of Reflections(R-Work) 7217
    R-Factor(R-Work) 0.1669
    R-Factor(R-Free) 0.1977
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 10.0575
    Shell Resolution(Low) 44.393
    Number of Reflections(R-Free) 382
    Number of Reflections(R-Work) 7234
    R-Factor(R-Work) 0.2187
    R-Factor(R-Free) 0.2323
    Percent Reflections(Observed) 94.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 24.789
    f_plane_restr 0.006
    f_chiral_restr 0.068
    f_angle_d 1.032
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 19143
    Nucleic Acid Atoms 32504
    Heterogen Atoms 1037
    Solvent Atoms 537
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution PHENIX (phenix.refine: dev_978)
    Structure Refinement PHENIX (phenix.refine: dev_978)
     
    Software
    data extraction pdb_extract version: 3.10
    refinement phenix
    data reduction SCALEPACK
    data collection DENZO