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X-RAY DIFFRACTION
Materials and Methods page
4JI1
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.5
    Temperature 277.0
    Details MPD , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 403.17 α = 90
    b = 403.17 β = 90
    c = 173.32 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 Monochromator
    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) 3.14
    Resolution(Low) 35
    Number Reflections(All) 241842
    Number Reflections(Observed) 241842
    Percent Possible(Observed) 99.0
    R Merge I(Observed) 0.069
    Redundancy 3.4
     
    High Resolution Shell Details
    Resolution(High) 3.14
    Resolution(Low) 3.25
    Percent Possible(All) 97.7
    R Merge I(Observed) 0.627
    Redundancy 3.4
    Number Unique Reflections(All) 23584
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 3.144
    Resolution(Low) 34.647
    Cut-off Sigma(F) 1.34
    Number of Reflections(all) 241726
    Number of Reflections(Observed) 241726
    Number of Reflections(R-Free) 12240
    Percent Reflections(Observed) 98.65
    R-Factor(Observed) 0.1667
    R-Work 0.1646
    R-Free 0.207
    R-Free Selection Details FROM PDB ENTRY 2VQE
     
    Temperature Factor Modeling
    Mean Isotropic B Value 122.024
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.144
    Shell Resolution(Low) 3.1798
    Number of Reflections(R-Free) 373
    Number of Reflections(R-Work) 6294
    R-Factor(R-Work) 0.2952
    R-Factor(R-Free) 0.3293
    Percent Reflections(Observed) 83.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1798
    Shell Resolution(Low) 3.2171
    Number of Reflections(R-Free) 398
    Number of Reflections(R-Work) 7620
    R-Factor(R-Work) 0.2821
    R-Factor(R-Free) 0.3168
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2171
    Shell Resolution(Low) 3.2563
    Number of Reflections(R-Free) 428
    Number of Reflections(R-Work) 7658
    R-Factor(R-Work) 0.2644
    R-Factor(R-Free) 0.3029
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2563
    Shell Resolution(Low) 3.2975
    Number of Reflections(R-Free) 418
    Number of Reflections(R-Work) 7616
    R-Factor(R-Work) 0.2596
    R-Factor(R-Free) 0.3026
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2975
    Shell Resolution(Low) 3.3409
    Number of Reflections(R-Free) 415
    Number of Reflections(R-Work) 7648
    R-Factor(R-Work) 0.2463
    R-Factor(R-Free) 0.2938
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3409
    Shell Resolution(Low) 3.3866
    Number of Reflections(R-Free) 404
    Number of Reflections(R-Work) 7689
    R-Factor(R-Work) 0.2329
    R-Factor(R-Free) 0.2883
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3866
    Shell Resolution(Low) 3.435
    Number of Reflections(R-Free) 428
    Number of Reflections(R-Work) 7605
    R-Factor(R-Work) 0.2316
    R-Factor(R-Free) 0.2813
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.435
    Shell Resolution(Low) 3.4862
    Number of Reflections(R-Free) 436
    Number of Reflections(R-Work) 7631
    R-Factor(R-Work) 0.2245
    R-Factor(R-Free) 0.2695
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4862
    Shell Resolution(Low) 3.5406
    Number of Reflections(R-Free) 421
    Number of Reflections(R-Work) 7707
    R-Factor(R-Work) 0.2021
    R-Factor(R-Free) 0.2471
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5406
    Shell Resolution(Low) 3.5986
    Number of Reflections(R-Free) 418
    Number of Reflections(R-Work) 7651
    R-Factor(R-Work) 0.1926
    R-Factor(R-Free) 0.2307
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5986
    Shell Resolution(Low) 3.6606
    Number of Reflections(R-Free) 404
    Number of Reflections(R-Work) 7660
    R-Factor(R-Work) 0.1848
    R-Factor(R-Free) 0.2265
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6606
    Shell Resolution(Low) 3.7271
    Number of Reflections(R-Free) 419
    Number of Reflections(R-Work) 7668
    R-Factor(R-Work) 0.1775
    R-Factor(R-Free) 0.2305
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7271
    Shell Resolution(Low) 3.7987
    Number of Reflections(R-Free) 424
    Number of Reflections(R-Work) 7677
    R-Factor(R-Work) 0.1664
    R-Factor(R-Free) 0.2191
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7987
    Shell Resolution(Low) 3.8761
    Number of Reflections(R-Free) 379
    Number of Reflections(R-Work) 7735
    R-Factor(R-Work) 0.1585
    R-Factor(R-Free) 0.1997
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8761
    Shell Resolution(Low) 3.9603
    Number of Reflections(R-Free) 404
    Number of Reflections(R-Work) 7682
    R-Factor(R-Work) 0.1482
    R-Factor(R-Free) 0.1885
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9603
    Shell Resolution(Low) 4.0523
    Number of Reflections(R-Free) 420
    Number of Reflections(R-Work) 7690
    R-Factor(R-Work) 0.1442
    R-Factor(R-Free) 0.1856
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0523
    Shell Resolution(Low) 4.1534
    Number of Reflections(R-Free) 420
    Number of Reflections(R-Work) 7714
    R-Factor(R-Work) 0.1485
    R-Factor(R-Free) 0.1963
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1534
    Shell Resolution(Low) 4.2655
    Number of Reflections(R-Free) 372
    Number of Reflections(R-Work) 7739
    R-Factor(R-Work) 0.145
    R-Factor(R-Free) 0.2016
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2655
    Shell Resolution(Low) 4.3908
    Number of Reflections(R-Free) 437
    Number of Reflections(R-Work) 7726
    R-Factor(R-Work) 0.1441
    R-Factor(R-Free) 0.185
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3908
    Shell Resolution(Low) 4.5322
    Number of Reflections(R-Free) 438
    Number of Reflections(R-Work) 7706
    R-Factor(R-Work) 0.1429
    R-Factor(R-Free) 0.1861
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5322
    Shell Resolution(Low) 4.6939
    Number of Reflections(R-Free) 374
    Number of Reflections(R-Work) 7777
    R-Factor(R-Work) 0.1397
    R-Factor(R-Free) 0.1837
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6939
    Shell Resolution(Low) 4.8813
    Number of Reflections(R-Free) 397
    Number of Reflections(R-Work) 7756
    R-Factor(R-Work) 0.1328
    R-Factor(R-Free) 0.1769
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8813
    Shell Resolution(Low) 5.1028
    Number of Reflections(R-Free) 414
    Number of Reflections(R-Work) 7770
    R-Factor(R-Work) 0.13
    R-Factor(R-Free) 0.1758
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1028
    Shell Resolution(Low) 5.3709
    Number of Reflections(R-Free) 381
    Number of Reflections(R-Work) 7761
    R-Factor(R-Work) 0.1277
    R-Factor(R-Free) 0.1785
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.3709
    Shell Resolution(Low) 5.706
    Number of Reflections(R-Free) 412
    Number of Reflections(R-Work) 7748
    R-Factor(R-Work) 0.137
    R-Factor(R-Free) 0.1903
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.706
    Shell Resolution(Low) 6.1443
    Number of Reflections(R-Free) 386
    Number of Reflections(R-Work) 7824
    R-Factor(R-Work) 0.1416
    R-Factor(R-Free) 0.2037
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.1443
    Shell Resolution(Low) 6.7585
    Number of Reflections(R-Free) 413
    Number of Reflections(R-Work) 7758
    R-Factor(R-Work) 0.1428
    R-Factor(R-Free) 0.1803
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.7585
    Shell Resolution(Low) 7.727
    Number of Reflections(R-Free) 402
    Number of Reflections(R-Work) 7781
    R-Factor(R-Work) 0.1411
    R-Factor(R-Free) 0.1866
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.727
    Shell Resolution(Low) 9.6997
    Number of Reflections(R-Free) 410
    Number of Reflections(R-Work) 7646
    R-Factor(R-Work) 0.1584
    R-Factor(R-Free) 0.1827
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 9.6997
    Shell Resolution(Low) 34.6489
    Number of Reflections(R-Free) 395
    Number of Reflections(R-Work) 7549
    R-Factor(R-Work) 0.1858
    R-Factor(R-Free) 0.2033
    Percent Reflections(Observed) 92.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 18.022
    f_plane_restr 0.006
    f_chiral_restr 0.068
    f_angle_d 1.212
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 19169
    Nucleic Acid Atoms 32507
    Heterogen Atoms 367
    Solvent Atoms 733
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution PHENIX (phenix.refine: dev_1119)
    Structure Refinement PHENIX (phenix.refine: dev_1119)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction SCALEPACK
    data collection DENZO