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X-RAY DIFFRACTION
Materials and Methods page
4DV7
  •   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 = 403.37 α = 90
    b = 403.37 β = 90
    c = 173.6 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 2010-11-07
     
    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) 3.29
    Resolution(Low) 35
    Number Reflections(All) 210955
    Number Reflections(Observed) 210955
    Percent Possible(Observed) 98.8
    R Merge I(Observed) 0.091
    Redundancy 4.8
     
    High Resolution Shell Details
    Resolution(High) 3.294
    Resolution(Low) 3.42
    Percent Possible(All) 99.9
    R Merge I(Observed) 0.875
    Redundancy 4.6
    Number Unique Reflections(All) 21141
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 3.294
    Resolution(Low) 34.924
    Cut-off Sigma(F) 1.34
    Number of Reflections(all) 210877
    Number of Reflections(Observed) 210877
    Number of Reflections(R-Free) 10630
    Percent Reflections(Observed) 98.6
    R-Factor(Observed) 0.1698
    R-Work 0.1677
    R-Free 0.2103
    R-Free Selection Details FROM PDB ENTRY 2VQE
     
    Temperature Factor Modeling
    Mean Isotropic B Value 161.233
    Anisotropic B[1][1] -13.3959
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -13.3959
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 11.1228
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.294
    Shell Resolution(Low) 3.3317
    Number of Reflections(R-Free) 360
    Number of Reflections(R-Work) 6240
    R-Factor(R-Work) 0.3065
    R-Factor(R-Free) 0.3557
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3317
    Shell Resolution(Low) 3.3708
    Number of Reflections(R-Free) 336
    Number of Reflections(R-Work) 6677
    R-Factor(R-Work) 0.279
    R-Factor(R-Free) 0.308
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3708
    Shell Resolution(Low) 3.4119
    Number of Reflections(R-Free) 384
    Number of Reflections(R-Work) 6673
    R-Factor(R-Work) 0.2769
    R-Factor(R-Free) 0.3451
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4119
    Shell Resolution(Low) 3.455
    Number of Reflections(R-Free) 360
    Number of Reflections(R-Work) 6683
    R-Factor(R-Work) 0.2621
    R-Factor(R-Free) 0.291
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.455
    Shell Resolution(Low) 3.5005
    Number of Reflections(R-Free) 369
    Number of Reflections(R-Work) 6626
    R-Factor(R-Work) 0.2489
    R-Factor(R-Free) 0.3024
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5005
    Shell Resolution(Low) 3.5484
    Number of Reflections(R-Free) 361
    Number of Reflections(R-Work) 6720
    R-Factor(R-Work) 0.2394
    R-Factor(R-Free) 0.2852
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5484
    Shell Resolution(Low) 3.599
    Number of Reflections(R-Free) 376
    Number of Reflections(R-Work) 6682
    R-Factor(R-Work) 0.2252
    R-Factor(R-Free) 0.2464
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.599
    Shell Resolution(Low) 3.6527
    Number of Reflections(R-Free) 355
    Number of Reflections(R-Work) 6688
    R-Factor(R-Work) 0.218
    R-Factor(R-Free) 0.2487
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6527
    Shell Resolution(Low) 3.7097
    Number of Reflections(R-Free) 373
    Number of Reflections(R-Work) 6720
    R-Factor(R-Work) 0.2096
    R-Factor(R-Free) 0.2725
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7097
    Shell Resolution(Low) 3.7704
    Number of Reflections(R-Free) 379
    Number of Reflections(R-Work) 6704
    R-Factor(R-Work) 0.1994
    R-Factor(R-Free) 0.246
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7704
    Shell Resolution(Low) 3.8354
    Number of Reflections(R-Free) 314
    Number of Reflections(R-Work) 6735
    R-Factor(R-Work) 0.1935
    R-Factor(R-Free) 0.2558
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8354
    Shell Resolution(Low) 3.905
    Number of Reflections(R-Free) 353
    Number of Reflections(R-Work) 6705
    R-Factor(R-Work) 0.1803
    R-Factor(R-Free) 0.2053
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.905
    Shell Resolution(Low) 3.98
    Number of Reflections(R-Free) 345
    Number of Reflections(R-Work) 6736
    R-Factor(R-Work) 0.178
    R-Factor(R-Free) 0.2238
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.98
    Shell Resolution(Low) 4.0612
    Number of Reflections(R-Free) 376
    Number of Reflections(R-Work) 6708
    R-Factor(R-Work) 0.1688
    R-Factor(R-Free) 0.2186
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0612
    Shell Resolution(Low) 4.1493
    Number of Reflections(R-Free) 376
    Number of Reflections(R-Work) 6686
    R-Factor(R-Work) 0.1627
    R-Factor(R-Free) 0.204
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1493
    Shell Resolution(Low) 4.2457
    Number of Reflections(R-Free) 330
    Number of Reflections(R-Work) 6762
    R-Factor(R-Work) 0.1546
    R-Factor(R-Free) 0.2129
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2457
    Shell Resolution(Low) 4.3517
    Number of Reflections(R-Free) 379
    Number of Reflections(R-Work) 6695
    R-Factor(R-Work) 0.1579
    R-Factor(R-Free) 0.2099
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3517
    Shell Resolution(Low) 4.4691
    Number of Reflections(R-Free) 367
    Number of Reflections(R-Work) 6711
    R-Factor(R-Work) 0.1542
    R-Factor(R-Free) 0.2025
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4691
    Shell Resolution(Low) 4.6003
    Number of Reflections(R-Free) 355
    Number of Reflections(R-Work) 6720
    R-Factor(R-Work) 0.1484
    R-Factor(R-Free) 0.1982
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6003
    Shell Resolution(Low) 4.7485
    Number of Reflections(R-Free) 324
    Number of Reflections(R-Work) 6759
    R-Factor(R-Work) 0.145
    R-Factor(R-Free) 0.1849
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7485
    Shell Resolution(Low) 4.9177
    Number of Reflections(R-Free) 347
    Number of Reflections(R-Work) 6733
    R-Factor(R-Work) 0.1398
    R-Factor(R-Free) 0.1834
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9177
    Shell Resolution(Low) 5.1141
    Number of Reflections(R-Free) 358
    Number of Reflections(R-Work) 6744
    R-Factor(R-Work) 0.1343
    R-Factor(R-Free) 0.1817
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1141
    Shell Resolution(Low) 5.346
    Number of Reflections(R-Free) 335
    Number of Reflections(R-Work) 6724
    R-Factor(R-Work) 0.1369
    R-Factor(R-Free) 0.1815
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.346
    Shell Resolution(Low) 5.6268
    Number of Reflections(R-Free) 361
    Number of Reflections(R-Work) 6708
    R-Factor(R-Work) 0.1366
    R-Factor(R-Free) 0.1966
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.6268
    Shell Resolution(Low) 5.9777
    Number of Reflections(R-Free) 333
    Number of Reflections(R-Work) 6713
    R-Factor(R-Work) 0.1429
    R-Factor(R-Free) 0.1989
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.9777
    Shell Resolution(Low) 6.4366
    Number of Reflections(R-Free) 334
    Number of Reflections(R-Work) 6723
    R-Factor(R-Work) 0.1459
    R-Factor(R-Free) 0.1813
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.4366
    Shell Resolution(Low) 7.0795
    Number of Reflections(R-Free) 349
    Number of Reflections(R-Work) 6675
    R-Factor(R-Work) 0.1398
    R-Factor(R-Free) 0.1894
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.0795
    Shell Resolution(Low) 8.0927
    Number of Reflections(R-Free) 335
    Number of Reflections(R-Work) 6682
    R-Factor(R-Work) 0.141
    R-Factor(R-Free) 0.1931
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.0927
    Shell Resolution(Low) 10.1543
    Number of Reflections(R-Free) 373
    Number of Reflections(R-Work) 6678
    R-Factor(R-Work) 0.1533
    R-Factor(R-Free) 0.1848
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 10.1543
    Shell Resolution(Low) 34.9259
    Number of Reflections(R-Free) 333
    Number of Reflections(R-Work) 6237
    R-Factor(R-Work) 0.197
    R-Factor(R-Free) 0.2135
    Percent Reflections(Observed) 87.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 18.282
    f_plane_restr 0.006
    f_chiral_restr 0.07
    f_angle_d 1.022
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 19088
    Nucleic Acid Atoms 32508
    Heterogen Atoms 334
    Solvent Atoms 407
     
     
  •   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