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X-RAY DIFFRACTION
Materials and Methods page
4JI8
  •   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 = 400.3 α = 90
    b = 400.3 β = 90
    c = 214.79 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 PIXEL
    Type DECTRIS PILATUS 6M
    Collection Date 2011-02-06
     
    Diffraction Radiation
    Monochromator LN2 cooled fixed-exit Si(111) monochromator
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SLS BEAMLINE X06SA
    Wavelength List 0.98
    Site SLS
    Beamline X06SA
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) -3.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 3.74
    Resolution(Low) 50
    Number Reflections(All) 177718
    Number Reflections(Observed) 177718
    Percent Possible(Observed) 99.7
    R Merge I(Observed) 0.132
    B(Isotropic) From Wilson Plot 138.037
     
    High Resolution Shell Details
    Resolution(High) 3.74
    Resolution(Low) 3.97
    Percent Possible(All) 98.3
    R Merge I(Observed) 0.016
    Mean I Over Sigma(Observed) 1.87
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 3.742
    Resolution(Low) 49.854
    Cut-off Sigma(F) 1.99
    Number of Reflections(all) 177681
    Number of Reflections(Observed) 177681
    Number of Reflections(R-Free) 8970
    Percent Reflections(Observed) 99.71
    R-Factor(All) 0.1393
    R-Factor(Observed) 0.1393
    R-Work 0.1368
    R-Free 0.1873
    R-Free Selection Details FROM PDB ENTRY 2VQE
     
    Temperature Factor Modeling
    Mean Isotropic B Value 154.619
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.742
    Shell Resolution(Low) 3.7845
    Number of Reflections(R-Free) 296
    Number of Reflections(R-Work) 5103
    R-Factor(R-Work) 0.2674
    R-Factor(R-Free) 0.3159
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7845
    Shell Resolution(Low) 3.829
    Number of Reflections(R-Free) 301
    Number of Reflections(R-Work) 5581
    R-Factor(R-Work) 0.2414
    R-Factor(R-Free) 0.2971
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.829
    Shell Resolution(Low) 3.8757
    Number of Reflections(R-Free) 330
    Number of Reflections(R-Work) 5533
    R-Factor(R-Work) 0.2285
    R-Factor(R-Free) 0.2817
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8757
    Shell Resolution(Low) 3.9247
    Number of Reflections(R-Free) 307
    Number of Reflections(R-Work) 5582
    R-Factor(R-Work) 0.2425
    R-Factor(R-Free) 0.3057
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9247
    Shell Resolution(Low) 3.9764
    Number of Reflections(R-Free) 299
    Number of Reflections(R-Work) 5573
    R-Factor(R-Work) 0.2115
    R-Factor(R-Free) 0.2891
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9764
    Shell Resolution(Low) 4.0308
    Number of Reflections(R-Free) 311
    Number of Reflections(R-Work) 5542
    R-Factor(R-Work) 0.1948
    R-Factor(R-Free) 0.2497
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0308
    Shell Resolution(Low) 4.0884
    Number of Reflections(R-Free) 279
    Number of Reflections(R-Work) 5643
    R-Factor(R-Work) 0.1812
    R-Factor(R-Free) 0.237
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0884
    Shell Resolution(Low) 4.1494
    Number of Reflections(R-Free) 316
    Number of Reflections(R-Work) 5542
    R-Factor(R-Work) 0.1646
    R-Factor(R-Free) 0.234
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1494
    Shell Resolution(Low) 4.2142
    Number of Reflections(R-Free) 292
    Number of Reflections(R-Work) 5621
    R-Factor(R-Work) 0.1662
    R-Factor(R-Free) 0.239
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2142
    Shell Resolution(Low) 4.2832
    Number of Reflections(R-Free) 283
    Number of Reflections(R-Work) 5592
    R-Factor(R-Work) 0.157
    R-Factor(R-Free) 0.2283
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2832
    Shell Resolution(Low) 4.357
    Number of Reflections(R-Free) 283
    Number of Reflections(R-Work) 5623
    R-Factor(R-Work) 0.141
    R-Factor(R-Free) 0.1894
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.357
    Shell Resolution(Low) 4.4362
    Number of Reflections(R-Free) 319
    Number of Reflections(R-Work) 5549
    R-Factor(R-Work) 0.1371
    R-Factor(R-Free) 0.207
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4362
    Shell Resolution(Low) 4.5215
    Number of Reflections(R-Free) 247
    Number of Reflections(R-Work) 5655
    R-Factor(R-Work) 0.1412
    R-Factor(R-Free) 0.2083
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5215
    Shell Resolution(Low) 4.6137
    Number of Reflections(R-Free) 278
    Number of Reflections(R-Work) 5625
    R-Factor(R-Work) 0.1356
    R-Factor(R-Free) 0.1922
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6137
    Shell Resolution(Low) 4.714
    Number of Reflections(R-Free) 315
    Number of Reflections(R-Work) 5590
    R-Factor(R-Work) 0.1193
    R-Factor(R-Free) 0.1722
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.714
    Shell Resolution(Low) 4.8235
    Number of Reflections(R-Free) 287
    Number of Reflections(R-Work) 5617
    R-Factor(R-Work) 0.1062
    R-Factor(R-Free) 0.1677
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8235
    Shell Resolution(Low) 4.9441
    Number of Reflections(R-Free) 285
    Number of Reflections(R-Work) 5640
    R-Factor(R-Work) 0.1043
    R-Factor(R-Free) 0.1513
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9441
    Shell Resolution(Low) 5.0776
    Number of Reflections(R-Free) 276
    Number of Reflections(R-Work) 5628
    R-Factor(R-Work) 0.1016
    R-Factor(R-Free) 0.1477
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0776
    Shell Resolution(Low) 5.2269
    Number of Reflections(R-Free) 316
    Number of Reflections(R-Work) 5627
    R-Factor(R-Work) 0.1013
    R-Factor(R-Free) 0.1505
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2269
    Shell Resolution(Low) 5.3954
    Number of Reflections(R-Free) 292
    Number of Reflections(R-Work) 5636
    R-Factor(R-Work) 0.1025
    R-Factor(R-Free) 0.1697
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.3954
    Shell Resolution(Low) 5.588
    Number of Reflections(R-Free) 305
    Number of Reflections(R-Work) 5616
    R-Factor(R-Work) 0.0984
    R-Factor(R-Free) 0.1557
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.588
    Shell Resolution(Low) 5.8114
    Number of Reflections(R-Free) 268
    Number of Reflections(R-Work) 5711
    R-Factor(R-Work) 0.0938
    R-Factor(R-Free) 0.1389
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.8114
    Shell Resolution(Low) 6.0754
    Number of Reflections(R-Free) 298
    Number of Reflections(R-Work) 5635
    R-Factor(R-Work) 0.1022
    R-Factor(R-Free) 0.1517
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.0754
    Shell Resolution(Low) 6.3951
    Number of Reflections(R-Free) 320
    Number of Reflections(R-Work) 5645
    R-Factor(R-Work) 0.1014
    R-Factor(R-Free) 0.1695
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.3951
    Shell Resolution(Low) 6.7949
    Number of Reflections(R-Free) 306
    Number of Reflections(R-Work) 5663
    R-Factor(R-Work) 0.0986
    R-Factor(R-Free) 0.1459
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.7949
    Shell Resolution(Low) 7.318
    Number of Reflections(R-Free) 298
    Number of Reflections(R-Work) 5696
    R-Factor(R-Work) 0.1028
    R-Factor(R-Free) 0.1718
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.318
    Shell Resolution(Low) 8.0517
    Number of Reflections(R-Free) 298
    Number of Reflections(R-Work) 5725
    R-Factor(R-Work) 0.1059
    R-Factor(R-Free) 0.1573
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.0517
    Shell Resolution(Low) 9.2104
    Number of Reflections(R-Free) 311
    Number of Reflections(R-Work) 5730
    R-Factor(R-Work) 0.1209
    R-Factor(R-Free) 0.1643
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 9.2104
    Shell Resolution(Low) 11.5802
    Number of Reflections(R-Free) 322
    Number of Reflections(R-Work) 5793
    R-Factor(R-Work) 0.1342
    R-Factor(R-Free) 0.1756
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 11.5802
    Shell Resolution(Low) 49.8584
    Number of Reflections(R-Free) 332
    Number of Reflections(R-Work) 5995
    R-Factor(R-Work) 0.1984
    R-Factor(R-Free) 0.2172
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 21.31
    f_plane_restr 0.013
    f_chiral_restr 0.138
    f_angle_d 2.95
    f_bond_d 0.022
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 19093
    Nucleic Acid Atoms 32550
    Heterogen Atoms 456
    Solvent Atoms 1464
     
     
  •   Software and Computing Hide
    Computing
    Data Collection XDS
    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