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X-RAY DIFFRACTION
Materials and Methods page
4DV6
  •   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 = 401.25 α = 90
    b = 401.25 β = 90
    c = 176.04 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) 3.3
    Resolution(Low) 35
    Number Reflections(All) 210600
    Number Reflections(Observed) 210600
    Percent Possible(Observed) 98.9
    R Merge I(Observed) 0.097
    Redundancy 3.8
     
    High Resolution Shell Details
    Resolution(High) 3.297
    Resolution(Low) 3.42
    Percent Possible(All) 99.3
    R Merge I(Observed) 0.731
    Redundancy 3.8
    Number Unique Reflections(All) 20935
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 3.297
    Resolution(Low) 34.55
    Cut-off Sigma(F) 1.33
    Number of Reflections(all) 210495
    Number of Reflections(Observed) 210495
    Number of Reflections(R-Free) 10598
    Percent Reflections(Observed) 98.35
    R-Factor(Observed) 0.1654
    R-Work 0.1632
    R-Free 0.2076
    R-Free Selection Details FROM PDB ENTRY 2VQE
     
    Temperature Factor Modeling
    Mean Isotropic B Value 131.624
    Anisotropic B[1][1] -4.1015
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -4.1015
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 13.9121
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.297
    Shell Resolution(Low) 3.3345
    Number of Reflections(R-Free) 297
    Number of Reflections(R-Work) 5518
    R-Factor(R-Work) 0.2904
    R-Factor(R-Free) 0.3303
    Percent Reflections(Observed) 82.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3345
    Shell Resolution(Low) 3.3737
    Number of Reflections(R-Free) 345
    Number of Reflections(R-Work) 6666
    R-Factor(R-Work) 0.2813
    R-Factor(R-Free) 0.3232
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3737
    Shell Resolution(Low) 3.4148
    Number of Reflections(R-Free) 381
    Number of Reflections(R-Work) 6624
    R-Factor(R-Work) 0.2739
    R-Factor(R-Free) 0.3095
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4148
    Shell Resolution(Low) 3.458
    Number of Reflections(R-Free) 353
    Number of Reflections(R-Work) 6709
    R-Factor(R-Work) 0.2727
    R-Factor(R-Free) 0.3316
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.458
    Shell Resolution(Low) 3.5034
    Number of Reflections(R-Free) 365
    Number of Reflections(R-Work) 6702
    R-Factor(R-Work) 0.2538
    R-Factor(R-Free) 0.3107
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5034
    Shell Resolution(Low) 3.5514
    Number of Reflections(R-Free) 405
    Number of Reflections(R-Work) 6600
    R-Factor(R-Work) 0.2439
    R-Factor(R-Free) 0.2746
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5514
    Shell Resolution(Low) 3.602
    Number of Reflections(R-Free) 350
    Number of Reflections(R-Work) 6728
    R-Factor(R-Work) 0.2297
    R-Factor(R-Free) 0.2715
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.602
    Shell Resolution(Low) 3.6558
    Number of Reflections(R-Free) 342
    Number of Reflections(R-Work) 6716
    R-Factor(R-Work) 0.2188
    R-Factor(R-Free) 0.2678
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6558
    Shell Resolution(Low) 3.7128
    Number of Reflections(R-Free) 385
    Number of Reflections(R-Work) 6659
    R-Factor(R-Work) 0.2104
    R-Factor(R-Free) 0.2425
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7128
    Shell Resolution(Low) 3.7736
    Number of Reflections(R-Free) 374
    Number of Reflections(R-Work) 6637
    R-Factor(R-Work) 0.1947
    R-Factor(R-Free) 0.2517
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7736
    Shell Resolution(Low) 3.8386
    Number of Reflections(R-Free) 315
    Number of Reflections(R-Work) 6818
    R-Factor(R-Work) 0.1858
    R-Factor(R-Free) 0.2193
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8386
    Shell Resolution(Low) 3.9083
    Number of Reflections(R-Free) 360
    Number of Reflections(R-Work) 6660
    R-Factor(R-Work) 0.1854
    R-Factor(R-Free) 0.2469
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9083
    Shell Resolution(Low) 3.9834
    Number of Reflections(R-Free) 338
    Number of Reflections(R-Work) 6715
    R-Factor(R-Work) 0.1765
    R-Factor(R-Free) 0.2201
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9834
    Shell Resolution(Low) 4.0646
    Number of Reflections(R-Free) 377
    Number of Reflections(R-Work) 6692
    R-Factor(R-Work) 0.1696
    R-Factor(R-Free) 0.2227
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0646
    Shell Resolution(Low) 4.1528
    Number of Reflections(R-Free) 348
    Number of Reflections(R-Work) 6690
    R-Factor(R-Work) 0.1556
    R-Factor(R-Free) 0.2009
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1528
    Shell Resolution(Low) 4.2492
    Number of Reflections(R-Free) 350
    Number of Reflections(R-Work) 6728
    R-Factor(R-Work) 0.1526
    R-Factor(R-Free) 0.2173
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2492
    Shell Resolution(Low) 4.3553
    Number of Reflections(R-Free) 370
    Number of Reflections(R-Work) 6676
    R-Factor(R-Work) 0.1463
    R-Factor(R-Free) 0.1843
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3553
    Shell Resolution(Low) 4.4728
    Number of Reflections(R-Free) 371
    Number of Reflections(R-Work) 6701
    R-Factor(R-Work) 0.1411
    R-Factor(R-Free) 0.1845
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4728
    Shell Resolution(Low) 4.6041
    Number of Reflections(R-Free) 358
    Number of Reflections(R-Work) 6730
    R-Factor(R-Work) 0.1362
    R-Factor(R-Free) 0.1888
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6041
    Shell Resolution(Low) 4.7524
    Number of Reflections(R-Free) 317
    Number of Reflections(R-Work) 6738
    R-Factor(R-Work) 0.1342
    R-Factor(R-Free) 0.1803
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7524
    Shell Resolution(Low) 4.9218
    Number of Reflections(R-Free) 349
    Number of Reflections(R-Work) 6709
    R-Factor(R-Work) 0.124
    R-Factor(R-Free) 0.1825
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9218
    Shell Resolution(Low) 5.1182
    Number of Reflections(R-Free) 342
    Number of Reflections(R-Work) 6706
    R-Factor(R-Work) 0.1253
    R-Factor(R-Free) 0.1658
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1182
    Shell Resolution(Low) 5.3504
    Number of Reflections(R-Free) 352
    Number of Reflections(R-Work) 6778
    R-Factor(R-Work) 0.1235
    R-Factor(R-Free) 0.1678
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.3504
    Shell Resolution(Low) 5.6313
    Number of Reflections(R-Free) 346
    Number of Reflections(R-Work) 6710
    R-Factor(R-Work) 0.1309
    R-Factor(R-Free) 0.1979
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.6313
    Shell Resolution(Low) 5.9824
    Number of Reflections(R-Free) 354
    Number of Reflections(R-Work) 6756
    R-Factor(R-Work) 0.1358
    R-Factor(R-Free) 0.1842
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.9824
    Shell Resolution(Low) 6.4416
    Number of Reflections(R-Free) 333
    Number of Reflections(R-Work) 6753
    R-Factor(R-Work) 0.142
    R-Factor(R-Free) 0.1905
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.4416
    Shell Resolution(Low) 7.0848
    Number of Reflections(R-Free) 359
    Number of Reflections(R-Work) 6775
    R-Factor(R-Work) 0.1391
    R-Factor(R-Free) 0.1975
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.0848
    Shell Resolution(Low) 8.0985
    Number of Reflections(R-Free) 342
    Number of Reflections(R-Work) 6774
    R-Factor(R-Work) 0.1331
    R-Factor(R-Free) 0.1767
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.0985
    Shell Resolution(Low) 10.16
    Number of Reflections(R-Free) 367
    Number of Reflections(R-Work) 6697
    R-Factor(R-Work) 0.1536
    R-Factor(R-Free) 0.1813
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 10.16
    Shell Resolution(Low) 34.5517
    Number of Reflections(R-Free) 353
    Number of Reflections(R-Work) 6532
    R-Factor(R-Work) 0.1938
    R-Factor(R-Free) 0.2149
    Percent Reflections(Observed) 91.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 17.997
    f_plane_restr 0.005
    f_chiral_restr 0.067
    f_angle_d 0.979
    f_bond_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 19088
    Nucleic Acid Atoms 32508
    Heterogen Atoms 322
    Solvent Atoms 568
     
     
  •   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