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X-RAY DIFFRACTION
Materials and Methods page
4JI0
  •   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 = 403.74 α = 90
    b = 403.74 β = 90
    c = 174.34 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) 3.49
    Resolution(Low) 50
    Number Reflections(All) 179519
    Number Reflections(Observed) 179519
    Percent Possible(Observed) 99.1
    R Merge I(Observed) 0.077
    B(Isotropic) From Wilson Plot 116.443
     
    High Resolution Shell Details
    Resolution(High) 3.49
    Resolution(Low) 3.7
    Percent Possible(All) 96.4
    R Merge I(Observed) 0.763
    Mean I Over Sigma(Observed) 1.71
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 3.492
    Resolution(Low) 49.528
    Cut-off Sigma(F) 1.99
    Number of Reflections(all) 179494
    Number of Reflections(Observed) 179494
    Number of Reflections(R-Free) 9024
    Percent Reflections(Observed) 99.1
    R-Factor(Observed) 0.1692
    R-Work 0.167
    R-Free 0.2116
    R-Free Selection Details FROM PDB ENTRY 2VQE
     
    Temperature Factor Modeling
    Mean Isotropic B Value 168.292
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4917
    Shell Resolution(Low) 3.5314
    Number of Reflections(R-Free) 246
    Number of Reflections(R-Work) 4692
    R-Factor(R-Work) 0.3065
    R-Factor(R-Free) 0.3603
    Percent Reflections(Observed) 83.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5314
    Shell Resolution(Low) 3.5729
    Number of Reflections(R-Free) 299
    Number of Reflections(R-Work) 5680
    R-Factor(R-Work) 0.2797
    R-Factor(R-Free) 0.3223
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5729
    Shell Resolution(Low) 3.6165
    Number of Reflections(R-Free) 305
    Number of Reflections(R-Work) 5614
    R-Factor(R-Work) 0.2653
    R-Factor(R-Free) 0.3199
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6165
    Shell Resolution(Low) 3.6622
    Number of Reflections(R-Free) 328
    Number of Reflections(R-Work) 5646
    R-Factor(R-Work) 0.2535
    R-Factor(R-Free) 0.2956
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6622
    Shell Resolution(Low) 3.7104
    Number of Reflections(R-Free) 289
    Number of Reflections(R-Work) 5713
    R-Factor(R-Work) 0.2405
    R-Factor(R-Free) 0.2745
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7104
    Shell Resolution(Low) 3.7612
    Number of Reflections(R-Free) 326
    Number of Reflections(R-Work) 5626
    R-Factor(R-Work) 0.2275
    R-Factor(R-Free) 0.263
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7612
    Shell Resolution(Low) 3.8149
    Number of Reflections(R-Free) 290
    Number of Reflections(R-Work) 5689
    R-Factor(R-Work) 0.2118
    R-Factor(R-Free) 0.2673
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8149
    Shell Resolution(Low) 3.8718
    Number of Reflections(R-Free) 334
    Number of Reflections(R-Work) 5655
    R-Factor(R-Work) 0.2011
    R-Factor(R-Free) 0.2715
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8718
    Shell Resolution(Low) 3.9323
    Number of Reflections(R-Free) 272
    Number of Reflections(R-Work) 5709
    R-Factor(R-Work) 0.2043
    R-Factor(R-Free) 0.251
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9323
    Shell Resolution(Low) 3.9968
    Number of Reflections(R-Free) 309
    Number of Reflections(R-Work) 5658
    R-Factor(R-Work) 0.2045
    R-Factor(R-Free) 0.2532
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9968
    Shell Resolution(Low) 4.0657
    Number of Reflections(R-Free) 279
    Number of Reflections(R-Work) 5700
    R-Factor(R-Work) 0.1933
    R-Factor(R-Free) 0.2526
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0657
    Shell Resolution(Low) 4.1396
    Number of Reflections(R-Free) 297
    Number of Reflections(R-Work) 5693
    R-Factor(R-Work) 0.182
    R-Factor(R-Free) 0.2402
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1396
    Shell Resolution(Low) 4.2191
    Number of Reflections(R-Free) 303
    Number of Reflections(R-Work) 5675
    R-Factor(R-Work) 0.1691
    R-Factor(R-Free) 0.238
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2191
    Shell Resolution(Low) 4.3052
    Number of Reflections(R-Free) 292
    Number of Reflections(R-Work) 5695
    R-Factor(R-Work) 0.1688
    R-Factor(R-Free) 0.2121
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3052
    Shell Resolution(Low) 4.3988
    Number of Reflections(R-Free) 304
    Number of Reflections(R-Work) 5720
    R-Factor(R-Work) 0.1599
    R-Factor(R-Free) 0.2233
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3988
    Shell Resolution(Low) 4.501
    Number of Reflections(R-Free) 303
    Number of Reflections(R-Work) 5686
    R-Factor(R-Work) 0.1559
    R-Factor(R-Free) 0.1917
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.501
    Shell Resolution(Low) 4.6135
    Number of Reflections(R-Free) 270
    Number of Reflections(R-Work) 5731
    R-Factor(R-Work) 0.1447
    R-Factor(R-Free) 0.1937
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6135
    Shell Resolution(Low) 4.7381
    Number of Reflections(R-Free) 296
    Number of Reflections(R-Work) 5722
    R-Factor(R-Work) 0.1397
    R-Factor(R-Free) 0.2013
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7381
    Shell Resolution(Low) 4.8774
    Number of Reflections(R-Free) 301
    Number of Reflections(R-Work) 5689
    R-Factor(R-Work) 0.1376
    R-Factor(R-Free) 0.1803
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8774
    Shell Resolution(Low) 5.0347
    Number of Reflections(R-Free) 264
    Number of Reflections(R-Work) 5757
    R-Factor(R-Work) 0.1337
    R-Factor(R-Free) 0.191
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0347
    Shell Resolution(Low) 5.2145
    Number of Reflections(R-Free) 297
    Number of Reflections(R-Work) 5707
    R-Factor(R-Work) 0.1365
    R-Factor(R-Free) 0.1838
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2145
    Shell Resolution(Low) 5.423
    Number of Reflections(R-Free) 330
    Number of Reflections(R-Work) 5722
    R-Factor(R-Work) 0.1324
    R-Factor(R-Free) 0.1859
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.423
    Shell Resolution(Low) 5.6695
    Number of Reflections(R-Free) 286
    Number of Reflections(R-Work) 5748
    R-Factor(R-Work) 0.1317
    R-Factor(R-Free) 0.1881
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.6695
    Shell Resolution(Low) 5.9679
    Number of Reflections(R-Free) 325
    Number of Reflections(R-Work) 5733
    R-Factor(R-Work) 0.134
    R-Factor(R-Free) 0.1956
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.9679
    Shell Resolution(Low) 6.3411
    Number of Reflections(R-Free) 303
    Number of Reflections(R-Work) 5749
    R-Factor(R-Work) 0.1362
    R-Factor(R-Free) 0.2052
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.3411
    Shell Resolution(Low) 6.8296
    Number of Reflections(R-Free) 288
    Number of Reflections(R-Work) 5799
    R-Factor(R-Work) 0.1383
    R-Factor(R-Free) 0.1834
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.8296
    Shell Resolution(Low) 7.5148
    Number of Reflections(R-Free) 318
    Number of Reflections(R-Work) 5784
    R-Factor(R-Work) 0.1425
    R-Factor(R-Free) 0.1889
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.5148
    Shell Resolution(Low) 8.5973
    Number of Reflections(R-Free) 312
    Number of Reflections(R-Work) 5797
    R-Factor(R-Work) 0.1485
    R-Factor(R-Free) 0.1941
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.5973
    Shell Resolution(Low) 10.813
    Number of Reflections(R-Free) 324
    Number of Reflections(R-Work) 5811
    R-Factor(R-Work) 0.159
    R-Factor(R-Free) 0.2081
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 10.813
    Shell Resolution(Low) 49.5326
    Number of Reflections(R-Free) 334
    Number of Reflections(R-Work) 5870
    R-Factor(R-Work) 0.1953
    R-Factor(R-Free) 0.1922
    Percent Reflections(Observed) 96.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 18.074
    f_plane_restr 0.005
    f_chiral_restr 0.059
    f_angle_d 1.044
    f_bond_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 19089
    Nucleic Acid Atoms 32507
    Heterogen Atoms 308
    Solvent Atoms 275
     
     
  •   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