POP-OUT | CLOSE

An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4JI7
  •   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 = 397.81 α = 90
    b = 397.81 β = 90
    c = 214.91 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) 3.5
    Resolution(Low) 50
    Number Reflections(All) 214567
    Number Reflections(Observed) 214567
    Percent Possible(Observed) 99.6
    R Merge I(Observed) 0.12
    B(Isotropic) From Wilson Plot 109.741
     
    High Resolution Shell Details
    Resolution(High) 3.5
    Resolution(Low) 3.71
    Percent Possible(All) 97.6
    R Merge I(Observed) 0.988
    Mean I Over Sigma(Observed) 2.01
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 3.5
    Resolution(Low) 49.841
    Cut-off Sigma(F) 1.99
    Number of Reflections(all) 214519
    Number of Reflections(Observed) 214519
    Number of Reflections(R-Free) 10714
    Percent Reflections(Observed) 99.59
    R-Factor(Observed) 0.1604
    R-Work 0.1582
    R-Free 0.2011
    R-Free Selection Details 2VQE
     
    Temperature Factor Modeling
    Mean Isotropic B Value 116.778
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4965
    Shell Resolution(Low) 3.5362
    Number of Reflections(R-Free) 313
    Number of Reflections(R-Work) 6208
    R-Factor(R-Work) 0.2974
    R-Factor(R-Free) 0.3552
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5362
    Shell Resolution(Low) 3.5778
    Number of Reflections(R-Free) 324
    Number of Reflections(R-Work) 6661
    R-Factor(R-Work) 0.2737
    R-Factor(R-Free) 0.3249
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5778
    Shell Resolution(Low) 3.6215
    Number of Reflections(R-Free) 335
    Number of Reflections(R-Work) 6663
    R-Factor(R-Work) 0.245
    R-Factor(R-Free) 0.2926
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6215
    Shell Resolution(Low) 3.6673
    Number of Reflections(R-Free) 344
    Number of Reflections(R-Work) 6756
    R-Factor(R-Work) 0.2319
    R-Factor(R-Free) 0.2911
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6673
    Shell Resolution(Low) 3.7155
    Number of Reflections(R-Free) 336
    Number of Reflections(R-Work) 6795
    R-Factor(R-Work) 0.2251
    R-Factor(R-Free) 0.2703
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7155
    Shell Resolution(Low) 3.7664
    Number of Reflections(R-Free) 364
    Number of Reflections(R-Work) 6773
    R-Factor(R-Work) 0.2084
    R-Factor(R-Free) 0.274
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7664
    Shell Resolution(Low) 3.8202
    Number of Reflections(R-Free) 366
    Number of Reflections(R-Work) 6726
    R-Factor(R-Work) 0.1993
    R-Factor(R-Free) 0.2358
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8202
    Shell Resolution(Low) 3.8772
    Number of Reflections(R-Free) 404
    Number of Reflections(R-Work) 6709
    R-Factor(R-Work) 0.1883
    R-Factor(R-Free) 0.2348
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8772
    Shell Resolution(Low) 3.9378
    Number of Reflections(R-Free) 364
    Number of Reflections(R-Work) 6785
    R-Factor(R-Work) 0.1737
    R-Factor(R-Free) 0.2307
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9378
    Shell Resolution(Low) 4.0023
    Number of Reflections(R-Free) 371
    Number of Reflections(R-Work) 6723
    R-Factor(R-Work) 0.1674
    R-Factor(R-Free) 0.2204
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0023
    Shell Resolution(Low) 4.0713
    Number of Reflections(R-Free) 344
    Number of Reflections(R-Work) 6779
    R-Factor(R-Work) 0.1702
    R-Factor(R-Free) 0.227
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0713
    Shell Resolution(Low) 4.1453
    Number of Reflections(R-Free) 384
    Number of Reflections(R-Work) 6756
    R-Factor(R-Work) 0.154
    R-Factor(R-Free) 0.1973
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1453
    Shell Resolution(Low) 4.225
    Number of Reflections(R-Free) 337
    Number of Reflections(R-Work) 6790
    R-Factor(R-Work) 0.1514
    R-Factor(R-Free) 0.198
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.225
    Shell Resolution(Low) 4.3112
    Number of Reflections(R-Free) 346
    Number of Reflections(R-Work) 6782
    R-Factor(R-Work) 0.1481
    R-Factor(R-Free) 0.1978
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3112
    Shell Resolution(Low) 4.4048
    Number of Reflections(R-Free) 372
    Number of Reflections(R-Work) 6763
    R-Factor(R-Work) 0.1394
    R-Factor(R-Free) 0.1968
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4048
    Shell Resolution(Low) 4.5072
    Number of Reflections(R-Free) 306
    Number of Reflections(R-Work) 6852
    R-Factor(R-Work) 0.1353
    R-Factor(R-Free) 0.1744
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5072
    Shell Resolution(Low) 4.6199
    Number of Reflections(R-Free) 350
    Number of Reflections(R-Work) 6797
    R-Factor(R-Work) 0.1337
    R-Factor(R-Free) 0.1708
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6199
    Shell Resolution(Low) 4.7447
    Number of Reflections(R-Free) 371
    Number of Reflections(R-Work) 6760
    R-Factor(R-Work) 0.1284
    R-Factor(R-Free) 0.1718
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7447
    Shell Resolution(Low) 4.8842
    Number of Reflections(R-Free) 347
    Number of Reflections(R-Work) 6828
    R-Factor(R-Work) 0.1308
    R-Factor(R-Free) 0.176
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8842
    Shell Resolution(Low) 5.0417
    Number of Reflections(R-Free) 333
    Number of Reflections(R-Work) 6809
    R-Factor(R-Work) 0.1325
    R-Factor(R-Free) 0.1773
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0417
    Shell Resolution(Low) 5.2217
    Number of Reflections(R-Free) 381
    Number of Reflections(R-Work) 6803
    R-Factor(R-Work) 0.1289
    R-Factor(R-Free) 0.1717
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2217
    Shell Resolution(Low) 5.4305
    Number of Reflections(R-Free) 368
    Number of Reflections(R-Work) 6830
    R-Factor(R-Work) 0.128
    R-Factor(R-Free) 0.1843
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.4305
    Shell Resolution(Low) 5.6774
    Number of Reflections(R-Free) 343
    Number of Reflections(R-Work) 6864
    R-Factor(R-Work) 0.1255
    R-Factor(R-Free) 0.1781
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.6774
    Shell Resolution(Low) 5.9762
    Number of Reflections(R-Free) 343
    Number of Reflections(R-Work) 6869
    R-Factor(R-Work) 0.128
    R-Factor(R-Free) 0.1685
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.9762
    Shell Resolution(Low) 6.35
    Number of Reflections(R-Free) 381
    Number of Reflections(R-Work) 6829
    R-Factor(R-Work) 0.1306
    R-Factor(R-Free) 0.1897
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.35
    Shell Resolution(Low) 6.8391
    Number of Reflections(R-Free) 368
    Number of Reflections(R-Work) 6865
    R-Factor(R-Work) 0.1314
    R-Factor(R-Free) 0.1687
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.8391
    Shell Resolution(Low) 7.5253
    Number of Reflections(R-Free) 357
    Number of Reflections(R-Work) 6913
    R-Factor(R-Work) 0.1305
    R-Factor(R-Free) 0.1811
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.5253
    Shell Resolution(Low) 8.6093
    Number of Reflections(R-Free) 383
    Number of Reflections(R-Work) 6945
    R-Factor(R-Work) 0.1425
    R-Factor(R-Free) 0.1908
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.6093
    Shell Resolution(Low) 10.8285
    Number of Reflections(R-Free) 369
    Number of Reflections(R-Work) 6979
    R-Factor(R-Work) 0.1568
    R-Factor(R-Free) 0.1815
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 10.8285
    Shell Resolution(Low) 49.8459
    Number of Reflections(R-Free) 410
    Number of Reflections(R-Work) 7193
    R-Factor(R-Work) 0.2054
    R-Factor(R-Free) 0.2248
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 18.987
    f_plane_restr 0.007
    f_chiral_restr 0.078
    f_angle_d 1.439
    f_bond_d 0.009
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 19093
    Nucleic Acid Atoms 32550
    Heterogen Atoms 453
    Solvent Atoms 1577
     
     
  •   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