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X-RAY DIFFRACTION
Materials and Methods page
4JI4
  •   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 = 402.08 α = 90
    b = 402.08 β = 90
    c = 174.61 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) 3.69
    Resolution(Low) 50
    Number Reflections(All) 150281
    Number Reflections(Observed) 150281
    Percent Possible(Observed) 98.4
    R Merge I(Observed) 0.081
    B(Isotropic) From Wilson Plot 132.8
     
    High Resolution Shell Details
    Resolution(High) 3.69
    Resolution(Low) 3.91
    Percent Possible(All) 96.5
    R Merge I(Observed) 0.806
    Mean I Over Sigma(Observed) 1.79
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 3.692
    Resolution(Low) 48.299
    Cut-off Sigma(F) 1.99
    Number of Reflections(all) 150242
    Number of Reflections(Observed) 150242
    Number of Reflections(R-Free) 7538
    Percent Reflections(Observed) 98.48
    R-Factor(Observed) 0.1593
    R-Work 0.1564
    R-Free 0.214
    R-Free Selection Details FROM PDB ENTRY 2VQE
     
    Temperature Factor Modeling
    Mean Isotropic B Value 183.528
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6917
    Shell Resolution(Low) 3.7336
    Number of Reflections(R-Free) 218
    Number of Reflections(R-Work) 3979
    R-Factor(R-Work) 0.2896
    R-Factor(R-Free) 0.3258
    Percent Reflections(Observed) 84.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7336
    Shell Resolution(Low) 3.7775
    Number of Reflections(R-Free) 259
    Number of Reflections(R-Work) 4774
    R-Factor(R-Work) 0.2579
    R-Factor(R-Free) 0.3297
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7775
    Shell Resolution(Low) 3.8236
    Number of Reflections(R-Free) 278
    Number of Reflections(R-Work) 4718
    R-Factor(R-Work) 0.2459
    R-Factor(R-Free) 0.3004
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8236
    Shell Resolution(Low) 3.872
    Number of Reflections(R-Free) 284
    Number of Reflections(R-Work) 4762
    R-Factor(R-Work) 0.235
    R-Factor(R-Free) 0.2992
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.872
    Shell Resolution(Low) 3.9229
    Number of Reflections(R-Free) 209
    Number of Reflections(R-Work) 4807
    R-Factor(R-Work) 0.237
    R-Factor(R-Free) 0.2637
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9229
    Shell Resolution(Low) 3.9766
    Number of Reflections(R-Free) 257
    Number of Reflections(R-Work) 4799
    R-Factor(R-Work) 0.2206
    R-Factor(R-Free) 0.2799
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9766
    Shell Resolution(Low) 4.0334
    Number of Reflections(R-Free) 248
    Number of Reflections(R-Work) 4769
    R-Factor(R-Work) 0.2136
    R-Factor(R-Free) 0.2872
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0334
    Shell Resolution(Low) 4.0935
    Number of Reflections(R-Free) 233
    Number of Reflections(R-Work) 4798
    R-Factor(R-Work) 0.2157
    R-Factor(R-Free) 0.319
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0935
    Shell Resolution(Low) 4.1575
    Number of Reflections(R-Free) 253
    Number of Reflections(R-Work) 4797
    R-Factor(R-Work) 0.1983
    R-Factor(R-Free) 0.2821
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1575
    Shell Resolution(Low) 4.2256
    Number of Reflections(R-Free) 264
    Number of Reflections(R-Work) 4753
    R-Factor(R-Work) 0.1903
    R-Factor(R-Free) 0.2552
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2256
    Shell Resolution(Low) 4.2984
    Number of Reflections(R-Free) 235
    Number of Reflections(R-Work) 4787
    R-Factor(R-Work) 0.1767
    R-Factor(R-Free) 0.2393
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2984
    Shell Resolution(Low) 4.3765
    Number of Reflections(R-Free) 256
    Number of Reflections(R-Work) 4786
    R-Factor(R-Work) 0.171
    R-Factor(R-Free) 0.2499
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3765
    Shell Resolution(Low) 4.4607
    Number of Reflections(R-Free) 268
    Number of Reflections(R-Work) 4743
    R-Factor(R-Work) 0.164
    R-Factor(R-Free) 0.2226
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4607
    Shell Resolution(Low) 4.5516
    Number of Reflections(R-Free) 215
    Number of Reflections(R-Work) 4848
    R-Factor(R-Work) 0.1503
    R-Factor(R-Free) 0.2157
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5516
    Shell Resolution(Low) 4.6505
    Number of Reflections(R-Free) 246
    Number of Reflections(R-Work) 4779
    R-Factor(R-Work) 0.1479
    R-Factor(R-Free) 0.2228
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6505
    Shell Resolution(Low) 4.7586
    Number of Reflections(R-Free) 251
    Number of Reflections(R-Work) 4805
    R-Factor(R-Work) 0.138
    R-Factor(R-Free) 0.2162
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7586
    Shell Resolution(Low) 4.8775
    Number of Reflections(R-Free) 242
    Number of Reflections(R-Work) 4774
    R-Factor(R-Work) 0.1349
    R-Factor(R-Free) 0.1929
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8775
    Shell Resolution(Low) 5.0093
    Number of Reflections(R-Free) 223
    Number of Reflections(R-Work) 4802
    R-Factor(R-Work) 0.1322
    R-Factor(R-Free) 0.195
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0093
    Shell Resolution(Low) 5.1565
    Number of Reflections(R-Free) 262
    Number of Reflections(R-Work) 4795
    R-Factor(R-Work) 0.1281
    R-Factor(R-Free) 0.1963
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1565
    Shell Resolution(Low) 5.3227
    Number of Reflections(R-Free) 256
    Number of Reflections(R-Work) 4762
    R-Factor(R-Work) 0.1267
    R-Factor(R-Free) 0.1815
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.3227
    Shell Resolution(Low) 5.5127
    Number of Reflections(R-Free) 257
    Number of Reflections(R-Work) 4770
    R-Factor(R-Work) 0.1253
    R-Factor(R-Free) 0.1955
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.5127
    Shell Resolution(Low) 5.7331
    Number of Reflections(R-Free) 238
    Number of Reflections(R-Work) 4783
    R-Factor(R-Work) 0.1214
    R-Factor(R-Free) 0.1927
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.7331
    Shell Resolution(Low) 5.9936
    Number of Reflections(R-Free) 290
    Number of Reflections(R-Work) 4758
    R-Factor(R-Work) 0.1183
    R-Factor(R-Free) 0.1962
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.9936
    Shell Resolution(Low) 6.3089
    Number of Reflections(R-Free) 242
    Number of Reflections(R-Work) 4763
    R-Factor(R-Work) 0.1204
    R-Factor(R-Free) 0.1911
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.3089
    Shell Resolution(Low) 6.7032
    Number of Reflections(R-Free) 246
    Number of Reflections(R-Work) 4812
    R-Factor(R-Work) 0.1216
    R-Factor(R-Free) 0.1759
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.7032
    Shell Resolution(Low) 7.2192
    Number of Reflections(R-Free) 237
    Number of Reflections(R-Work) 4791
    R-Factor(R-Work) 0.1191
    R-Factor(R-Free) 0.1784
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.2192
    Shell Resolution(Low) 7.9429
    Number of Reflections(R-Free) 256
    Number of Reflections(R-Work) 4802
    R-Factor(R-Work) 0.1197
    R-Factor(R-Free) 0.1884
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.9429
    Shell Resolution(Low) 9.0856
    Number of Reflections(R-Free) 274
    Number of Reflections(R-Work) 4717
    R-Factor(R-Work) 0.1287
    R-Factor(R-Free) 0.1753
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 9.0856
    Shell Resolution(Low) 11.4218
    Number of Reflections(R-Free) 272
    Number of Reflections(R-Work) 4823
    R-Factor(R-Work) 0.141
    R-Factor(R-Free) 0.2021
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 11.4218
    Shell Resolution(Low) 48.3032
    Number of Reflections(R-Free) 269
    Number of Reflections(R-Work) 4848
    R-Factor(R-Work) 0.1969
    R-Factor(R-Free) 0.2146
    Percent Reflections(Observed) 94.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 20.048
    f_plane_restr 0.008
    f_chiral_restr 0.088
    f_angle_d 1.796
    f_bond_d 0.012
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 19089
    Nucleic Acid Atoms 32507
    Heterogen Atoms 276
    Solvent Atoms 272
     
     
  •   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