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X-RAY DIFFRACTION
Materials and Methods page
4JI6
  •   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 = 401.95 α = 90
    b = 401.95 β = 90
    c = 217.35 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 2011-08-03
     
    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) 3.55
    Resolution(Low) 50
    Number Reflections(All) 209634
    Number Reflections(Observed) 209634
    Percent Possible(Observed) 98.3
    R Merge I(Observed) 0.112
    B(Isotropic) From Wilson Plot 120.364
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 3.55
    Resolution(Low) 50.0
    Cut-off Sigma(F) 1.99
    Number of Reflections(all) 209597
    Number of Reflections(Observed) 209597
    Number of Reflections(R-Free) 10476
    Percent Reflections(Observed) 98.33
    R-Factor(Observed) 0.1535
    R-Work 0.151
    R-Free 0.201
    R-Free Selection Details PDB ENTRY 2VQE
     
    Temperature Factor Modeling
    Mean Isotropic B Value 142.922
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5463
    Shell Resolution(Low) 3.5866
    Number of Reflections(R-Free) 283
    Number of Reflections(R-Work) 5955
    R-Factor(R-Work) 0.282
    R-Factor(R-Free) 0.3387
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5866
    Shell Resolution(Low) 3.6288
    Number of Reflections(R-Free) 331
    Number of Reflections(R-Work) 6679
    R-Factor(R-Work) 0.2639
    R-Factor(R-Free) 0.3245
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6288
    Shell Resolution(Low) 3.673
    Number of Reflections(R-Free) 344
    Number of Reflections(R-Work) 6560
    R-Factor(R-Work) 0.2503
    R-Factor(R-Free) 0.314
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.673
    Shell Resolution(Low) 3.7195
    Number of Reflections(R-Free) 349
    Number of Reflections(R-Work) 6620
    R-Factor(R-Work) 0.2434
    R-Factor(R-Free) 0.3206
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7195
    Shell Resolution(Low) 3.7684
    Number of Reflections(R-Free) 314
    Number of Reflections(R-Work) 6614
    R-Factor(R-Work) 0.2263
    R-Factor(R-Free) 0.2858
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7684
    Shell Resolution(Low) 3.82
    Number of Reflections(R-Free) 367
    Number of Reflections(R-Work) 6639
    R-Factor(R-Work) 0.2168
    R-Factor(R-Free) 0.2782
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.82
    Shell Resolution(Low) 3.8746
    Number of Reflections(R-Free) 366
    Number of Reflections(R-Work) 6598
    R-Factor(R-Work) 0.2043
    R-Factor(R-Free) 0.2608
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8746
    Shell Resolution(Low) 3.9324
    Number of Reflections(R-Free) 373
    Number of Reflections(R-Work) 6579
    R-Factor(R-Work) 0.2037
    R-Factor(R-Free) 0.2715
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9324
    Shell Resolution(Low) 3.9938
    Number of Reflections(R-Free) 364
    Number of Reflections(R-Work) 6575
    R-Factor(R-Work) 0.2018
    R-Factor(R-Free) 0.2696
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9938
    Shell Resolution(Low) 4.0593
    Number of Reflections(R-Free) 366
    Number of Reflections(R-Work) 6608
    R-Factor(R-Work) 0.1911
    R-Factor(R-Free) 0.2541
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0593
    Shell Resolution(Low) 4.1292
    Number of Reflections(R-Free) 351
    Number of Reflections(R-Work) 6581
    R-Factor(R-Work) 0.1801
    R-Factor(R-Free) 0.2279
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1292
    Shell Resolution(Low) 4.2043
    Number of Reflections(R-Free) 362
    Number of Reflections(R-Work) 6612
    R-Factor(R-Work) 0.1747
    R-Factor(R-Free) 0.2286
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2043
    Shell Resolution(Low) 4.2851
    Number of Reflections(R-Free) 319
    Number of Reflections(R-Work) 6680
    R-Factor(R-Work) 0.1669
    R-Factor(R-Free) 0.232
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2851
    Shell Resolution(Low) 4.3725
    Number of Reflections(R-Free) 340
    Number of Reflections(R-Work) 6613
    R-Factor(R-Work) 0.1672
    R-Factor(R-Free) 0.2239
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3725
    Shell Resolution(Low) 4.4675
    Number of Reflections(R-Free) 366
    Number of Reflections(R-Work) 6600
    R-Factor(R-Work) 0.1628
    R-Factor(R-Free) 0.2108
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4675
    Shell Resolution(Low) 4.5714
    Number of Reflections(R-Free) 303
    Number of Reflections(R-Work) 6693
    R-Factor(R-Work) 0.1588
    R-Factor(R-Free) 0.2188
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5714
    Shell Resolution(Low) 4.6856
    Number of Reflections(R-Free) 340
    Number of Reflections(R-Work) 6637
    R-Factor(R-Work) 0.148
    R-Factor(R-Free) 0.2065
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6856
    Shell Resolution(Low) 4.8122
    Number of Reflections(R-Free) 366
    Number of Reflections(R-Work) 6634
    R-Factor(R-Work) 0.1413
    R-Factor(R-Free) 0.1925
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8122
    Shell Resolution(Low) 4.9537
    Number of Reflections(R-Free) 324
    Number of Reflections(R-Work) 6662
    R-Factor(R-Work) 0.1301
    R-Factor(R-Free) 0.1831
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9537
    Shell Resolution(Low) 5.1134
    Number of Reflections(R-Free) 337
    Number of Reflections(R-Work) 6648
    R-Factor(R-Work) 0.1302
    R-Factor(R-Free) 0.1767
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1134
    Shell Resolution(Low) 5.296
    Number of Reflections(R-Free) 373
    Number of Reflections(R-Work) 6640
    R-Factor(R-Work) 0.1223
    R-Factor(R-Free) 0.1715
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.296
    Shell Resolution(Low) 5.5078
    Number of Reflections(R-Free) 363
    Number of Reflections(R-Work) 6682
    R-Factor(R-Work) 0.1215
    R-Factor(R-Free) 0.1773
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.5078
    Shell Resolution(Low) 5.7581
    Number of Reflections(R-Free) 332
    Number of Reflections(R-Work) 6683
    R-Factor(R-Work) 0.1168
    R-Factor(R-Free) 0.1803
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.7581
    Shell Resolution(Low) 6.0612
    Number of Reflections(R-Free) 329
    Number of Reflections(R-Work) 6699
    R-Factor(R-Work) 0.1115
    R-Factor(R-Free) 0.1699
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.0612
    Shell Resolution(Low) 6.4402
    Number of Reflections(R-Free) 375
    Number of Reflections(R-Work) 6711
    R-Factor(R-Work) 0.1142
    R-Factor(R-Free) 0.1743
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.4402
    Shell Resolution(Low) 6.9363
    Number of Reflections(R-Free) 366
    Number of Reflections(R-Work) 6722
    R-Factor(R-Work) 0.11
    R-Factor(R-Free) 0.1686
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.9363
    Shell Resolution(Low) 7.6321
    Number of Reflections(R-Free) 341
    Number of Reflections(R-Work) 6725
    R-Factor(R-Work) 0.1064
    R-Factor(R-Free) 0.1593
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.6321
    Shell Resolution(Low) 8.7315
    Number of Reflections(R-Free) 374
    Number of Reflections(R-Work) 6751
    R-Factor(R-Work) 0.112
    R-Factor(R-Free) 0.1622
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.7315
    Shell Resolution(Low) 10.9816
    Number of Reflections(R-Free) 362
    Number of Reflections(R-Work) 6812
    R-Factor(R-Work) 0.1256
    R-Factor(R-Free) 0.1697
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 10.9816
    Shell Resolution(Low) 50.0841
    Number of Reflections(R-Free) 396
    Number of Reflections(R-Work) 6909
    R-Factor(R-Work) 0.178
    R-Factor(R-Free) 0.1968
    Percent Reflections(Observed) 96.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 21.212
    f_plane_restr 0.012
    f_chiral_restr 0.127
    f_angle_d 2.778
    f_bond_d 0.02
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 19089
    Nucleic Acid Atoms 32550
    Heterogen Atoms 403
    Solvent Atoms 1265
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    Data Reduction (intensity integration) XSCALE
    Data Reduction (data scaling) XSCALE
    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 Xscale