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X-RAY DIFFRACTION
Materials and Methods page
4DV4
  •   Crystallization Hide
    Crystallization Experiments
    Method HANGING DROP
    pH 6.5
    Temperature 277.0
    Details MPD, pH 6.5, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 402.64 α = 90
    b = 402.64 β = 90
    c = 174.75 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 2010-11-07
     
    Diffraction Radiation
    Monochromator Kohzu HLD8-24
    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) 3.65
    Resolution(Low) 35
    Number Reflections(All) 155290
    Number Reflections(Observed) 155290
    Percent Possible(Observed) 98.3
    R Merge I(Observed) 0.08
    Redundancy 3.2
     
    High Resolution Shell Details
    Resolution(High) 3.65
    Resolution(Low) 3.78
    Percent Possible(All) 99.5
    R Merge I(Observed) 0.686
    Redundancy 3.2
    Number Unique Reflections(All) 15521
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 3.651
    Resolution(Low) 34.661
    Cut-off Sigma(F) 1.33
    Number of Reflections(all) 155190
    Number of Reflections(Observed) 155190
    Number of Reflections(R-Free) 7744
    Percent Reflections(Observed) 98.2
    R-Factor(Observed) 0.1559
    R-Work 0.1531
    R-Free 0.2083
    R-Free Selection Details FROM PDB ENTRY 2VQE
     
    Temperature Factor Modeling
    Mean Isotropic B Value 168.777
    Anisotropic B[1][1] -6.6447
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -6.6447
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 6.993
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.651
    Shell Resolution(Low) 3.6925
    Number of Reflections(R-Free) 277
    Number of Reflections(R-Work) 4708
    R-Factor(R-Work) 0.2906
    R-Factor(R-Free) 0.3483
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6925
    Shell Resolution(Low) 3.7358
    Number of Reflections(R-Free) 256
    Number of Reflections(R-Work) 4930
    R-Factor(R-Work) 0.2734
    R-Factor(R-Free) 0.3231
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7358
    Shell Resolution(Low) 3.7813
    Number of Reflections(R-Free) 292
    Number of Reflections(R-Work) 4890
    R-Factor(R-Work) 0.2602
    R-Factor(R-Free) 0.3055
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7813
    Shell Resolution(Low) 3.8292
    Number of Reflections(R-Free) 210
    Number of Reflections(R-Work) 4940
    R-Factor(R-Work) 0.2423
    R-Factor(R-Free) 0.3178
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8292
    Shell Resolution(Low) 3.8795
    Number of Reflections(R-Free) 264
    Number of Reflections(R-Work) 4964
    R-Factor(R-Work) 0.2297
    R-Factor(R-Free) 0.2623
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8795
    Shell Resolution(Low) 3.9325
    Number of Reflections(R-Free) 268
    Number of Reflections(R-Work) 4914
    R-Factor(R-Work) 0.2314
    R-Factor(R-Free) 0.2962
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9325
    Shell Resolution(Low) 3.9887
    Number of Reflections(R-Free) 247
    Number of Reflections(R-Work) 4965
    R-Factor(R-Work) 0.2092
    R-Factor(R-Free) 0.2736
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9887
    Shell Resolution(Low) 4.0481
    Number of Reflections(R-Free) 280
    Number of Reflections(R-Work) 4874
    R-Factor(R-Work) 0.2019
    R-Factor(R-Free) 0.2532
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0481
    Shell Resolution(Low) 4.1113
    Number of Reflections(R-Free) 285
    Number of Reflections(R-Work) 4916
    R-Factor(R-Work) 0.1969
    R-Factor(R-Free) 0.2521
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1113
    Shell Resolution(Low) 4.1785
    Number of Reflections(R-Free) 241
    Number of Reflections(R-Work) 4966
    R-Factor(R-Work) 0.1774
    R-Factor(R-Free) 0.2301
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1785
    Shell Resolution(Low) 4.2505
    Number of Reflections(R-Free) 253
    Number of Reflections(R-Work) 4932
    R-Factor(R-Work) 0.1728
    R-Factor(R-Free) 0.2579
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2505
    Shell Resolution(Low) 4.3276
    Number of Reflections(R-Free) 260
    Number of Reflections(R-Work) 4896
    R-Factor(R-Work) 0.1626
    R-Factor(R-Free) 0.2307
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3276
    Shell Resolution(Low) 4.4107
    Number of Reflections(R-Free) 275
    Number of Reflections(R-Work) 4934
    R-Factor(R-Work) 0.1575
    R-Factor(R-Free) 0.2066
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4107
    Shell Resolution(Low) 4.5005
    Number of Reflections(R-Free) 292
    Number of Reflections(R-Work) 4906
    R-Factor(R-Work) 0.1488
    R-Factor(R-Free) 0.2068
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5005
    Shell Resolution(Low) 4.5982
    Number of Reflections(R-Free) 255
    Number of Reflections(R-Work) 4946
    R-Factor(R-Work) 0.1448
    R-Factor(R-Free) 0.2055
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5982
    Shell Resolution(Low) 4.7049
    Number of Reflections(R-Free) 238
    Number of Reflections(R-Work) 4938
    R-Factor(R-Work) 0.1416
    R-Factor(R-Free) 0.2043
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7049
    Shell Resolution(Low) 4.8223
    Number of Reflections(R-Free) 227
    Number of Reflections(R-Work) 4992
    R-Factor(R-Work) 0.1288
    R-Factor(R-Free) 0.1959
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8223
    Shell Resolution(Low) 4.9523
    Number of Reflections(R-Free) 280
    Number of Reflections(R-Work) 4912
    R-Factor(R-Work) 0.1206
    R-Factor(R-Free) 0.1914
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9523
    Shell Resolution(Low) 5.0976
    Number of Reflections(R-Free) 256
    Number of Reflections(R-Work) 4945
    R-Factor(R-Work) 0.117
    R-Factor(R-Free) 0.1736
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0976
    Shell Resolution(Low) 5.2616
    Number of Reflections(R-Free) 238
    Number of Reflections(R-Work) 4933
    R-Factor(R-Work) 0.1089
    R-Factor(R-Free) 0.1643
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2616
    Shell Resolution(Low) 5.4489
    Number of Reflections(R-Free) 253
    Number of Reflections(R-Work) 4958
    R-Factor(R-Work) 0.1112
    R-Factor(R-Free) 0.1703
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.4489
    Shell Resolution(Low) 5.6662
    Number of Reflections(R-Free) 265
    Number of Reflections(R-Work) 4931
    R-Factor(R-Work) 0.113
    R-Factor(R-Free) 0.1805
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.6662
    Shell Resolution(Low) 5.9229
    Number of Reflections(R-Free) 254
    Number of Reflections(R-Work) 4949
    R-Factor(R-Work) 0.1099
    R-Factor(R-Free) 0.1656
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.9229
    Shell Resolution(Low) 6.2334
    Number of Reflections(R-Free) 246
    Number of Reflections(R-Work) 4941
    R-Factor(R-Work) 0.1146
    R-Factor(R-Free) 0.1765
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.2334
    Shell Resolution(Low) 6.6215
    Number of Reflections(R-Free) 254
    Number of Reflections(R-Work) 4926
    R-Factor(R-Work) 0.1288
    R-Factor(R-Free) 0.1883
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.6215
    Shell Resolution(Low) 7.1286
    Number of Reflections(R-Free) 254
    Number of Reflections(R-Work) 4937
    R-Factor(R-Work) 0.1293
    R-Factor(R-Free) 0.1872
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.1286
    Shell Resolution(Low) 7.8385
    Number of Reflections(R-Free) 252
    Number of Reflections(R-Work) 4952
    R-Factor(R-Work) 0.12
    R-Factor(R-Free) 0.1877
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.8385
    Shell Resolution(Low) 8.9556
    Number of Reflections(R-Free) 259
    Number of Reflections(R-Work) 4900
    R-Factor(R-Work) 0.122
    R-Factor(R-Free) 0.1603
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.9556
    Shell Resolution(Low) 11.2192
    Number of Reflections(R-Free) 258
    Number of Reflections(R-Work) 4914
    R-Factor(R-Work) 0.1337
    R-Factor(R-Free) 0.1686
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 11.2192
    Shell Resolution(Low) 34.6624
    Number of Reflections(R-Free) 255
    Number of Reflections(R-Work) 4637
    R-Factor(R-Work) 0.2087
    R-Factor(R-Free) 0.2492
    Percent Reflections(Observed) 87.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 19.908
    f_plane_restr 0.009
    f_chiral_restr 0.091
    f_angle_d 1.62
    f_bond_d 0.013
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 19088
    Nucleic Acid Atoms 32508
    Heterogen Atoms 289
    Solvent Atoms 412
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution PHENIX (phenix.refine: dev_978)
    Structure Refinement PHENIX (phenix.refine: dev_978)
     
    Software
    data extraction pdb_extract version: 3.10
    refinement phenix
    data reduction SCALEPACK
    data collection DENZO