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X-RAY DIFFRACTION
Materials and Methods page
4DUZ
  •   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 = 402.52 α = 90
    b = 402.52 β = 90
    c = 173.98 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) 150484
    Number Reflections(Observed) 150484
    Percent Possible(Observed) 95.8
    R Merge I(Observed) 0.08
    Redundancy 3.0
     
    High Resolution Shell Details
    Resolution(High) 3.65
    Resolution(Low) 3.78
    Percent Possible(All) 97.6
    R Merge I(Observed) 0.519
    Redundancy 2.8
    Number Unique Reflections(All) 15146
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 3.651
    Resolution(Low) 34.561
    Cut-off Sigma(F) 1.33
    Number of Reflections(all) 150379
    Number of Reflections(Observed) 150379
    Number of Reflections(R-Free) 7501
    Percent Reflections(Observed) 95.63
    R-Factor(Observed) 0.1587
    R-Work 0.1556
    R-Free 0.216
    R-Free Selection Details FROM PDB ENTRY 2VQE
     
    Temperature Factor Modeling
    Mean Isotropic B Value 172.503
    Anisotropic B[1][1] -8.3745
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -8.3745
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 6.7012
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.651
    Shell Resolution(Low) 3.6928
    Number of Reflections(R-Free) 272
    Number of Reflections(R-Work) 4606
    R-Factor(R-Work) 0.2684
    R-Factor(R-Free) 0.33
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6928
    Shell Resolution(Low) 3.7362
    Number of Reflections(R-Free) 243
    Number of Reflections(R-Work) 4752
    R-Factor(R-Work) 0.2528
    R-Factor(R-Free) 0.3417
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7362
    Shell Resolution(Low) 3.7817
    Number of Reflections(R-Free) 270
    Number of Reflections(R-Work) 4829
    R-Factor(R-Work) 0.2394
    R-Factor(R-Free) 0.2845
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7817
    Shell Resolution(Low) 3.8295
    Number of Reflections(R-Free) 220
    Number of Reflections(R-Work) 4823
    R-Factor(R-Work) 0.2332
    R-Factor(R-Free) 0.2932
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8295
    Shell Resolution(Low) 3.8798
    Number of Reflections(R-Free) 257
    Number of Reflections(R-Work) 4821
    R-Factor(R-Work) 0.2246
    R-Factor(R-Free) 0.2742
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8798
    Shell Resolution(Low) 3.9329
    Number of Reflections(R-Free) 253
    Number of Reflections(R-Work) 4740
    R-Factor(R-Work) 0.2229
    R-Factor(R-Free) 0.3073
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9329
    Shell Resolution(Low) 3.989
    Number of Reflections(R-Free) 254
    Number of Reflections(R-Work) 4854
    R-Factor(R-Work) 0.2132
    R-Factor(R-Free) 0.2806
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.989
    Shell Resolution(Low) 4.0485
    Number of Reflections(R-Free) 268
    Number of Reflections(R-Work) 4797
    R-Factor(R-Work) 0.2048
    R-Factor(R-Free) 0.2734
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0485
    Shell Resolution(Low) 4.1116
    Number of Reflections(R-Free) 285
    Number of Reflections(R-Work) 4742
    R-Factor(R-Work) 0.1943
    R-Factor(R-Free) 0.2656
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1116
    Shell Resolution(Low) 4.1789
    Number of Reflections(R-Free) 230
    Number of Reflections(R-Work) 4817
    R-Factor(R-Work) 0.1798
    R-Factor(R-Free) 0.2359
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1789
    Shell Resolution(Low) 4.2509
    Number of Reflections(R-Free) 232
    Number of Reflections(R-Work) 4825
    R-Factor(R-Work) 0.1666
    R-Factor(R-Free) 0.2494
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2509
    Shell Resolution(Low) 4.328
    Number of Reflections(R-Free) 256
    Number of Reflections(R-Work) 4792
    R-Factor(R-Work) 0.1604
    R-Factor(R-Free) 0.2124
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.328
    Shell Resolution(Low) 4.4111
    Number of Reflections(R-Free) 260
    Number of Reflections(R-Work) 4750
    R-Factor(R-Work) 0.1633
    R-Factor(R-Free) 0.2186
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4111
    Shell Resolution(Low) 4.501
    Number of Reflections(R-Free) 286
    Number of Reflections(R-Work) 4757
    R-Factor(R-Work) 0.1614
    R-Factor(R-Free) 0.2355
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.501
    Shell Resolution(Low) 4.5986
    Number of Reflections(R-Free) 246
    Number of Reflections(R-Work) 4786
    R-Factor(R-Work) 0.1537
    R-Factor(R-Free) 0.2186
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5986
    Shell Resolution(Low) 4.7053
    Number of Reflections(R-Free) 228
    Number of Reflections(R-Work) 4839
    R-Factor(R-Work) 0.1423
    R-Factor(R-Free) 0.1983
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7053
    Shell Resolution(Low) 4.8227
    Number of Reflections(R-Free) 232
    Number of Reflections(R-Work) 4795
    R-Factor(R-Work) 0.1352
    R-Factor(R-Free) 0.2146
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8227
    Shell Resolution(Low) 4.9527
    Number of Reflections(R-Free) 272
    Number of Reflections(R-Work) 4741
    R-Factor(R-Work) 0.1234
    R-Factor(R-Free) 0.1807
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9527
    Shell Resolution(Low) 5.098
    Number of Reflections(R-Free) 242
    Number of Reflections(R-Work) 4787
    R-Factor(R-Work) 0.1218
    R-Factor(R-Free) 0.1881
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.098
    Shell Resolution(Low) 5.262
    Number of Reflections(R-Free) 233
    Number of Reflections(R-Work) 4789
    R-Factor(R-Work) 0.1216
    R-Factor(R-Free) 0.1935
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.262
    Shell Resolution(Low) 5.4494
    Number of Reflections(R-Free) 246
    Number of Reflections(R-Work) 4790
    R-Factor(R-Work) 0.1166
    R-Factor(R-Free) 0.1769
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.4494
    Shell Resolution(Low) 5.6667
    Number of Reflections(R-Free) 247
    Number of Reflections(R-Work) 4761
    R-Factor(R-Work) 0.1163
    R-Factor(R-Free) 0.1817
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.6667
    Shell Resolution(Low) 5.9234
    Number of Reflections(R-Free) 247
    Number of Reflections(R-Work) 4775
    R-Factor(R-Work) 0.1155
    R-Factor(R-Free) 0.1667
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.9234
    Shell Resolution(Low) 6.2339
    Number of Reflections(R-Free) 235
    Number of Reflections(R-Work) 4762
    R-Factor(R-Work) 0.1201
    R-Factor(R-Free) 0.1902
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.2339
    Shell Resolution(Low) 6.622
    Number of Reflections(R-Free) 248
    Number of Reflections(R-Work) 4753
    R-Factor(R-Work) 0.1292
    R-Factor(R-Free) 0.1996
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.622
    Shell Resolution(Low) 7.1291
    Number of Reflections(R-Free) 243
    Number of Reflections(R-Work) 4724
    R-Factor(R-Work) 0.1267
    R-Factor(R-Free) 0.1833
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.1291
    Shell Resolution(Low) 7.839
    Number of Reflections(R-Free) 241
    Number of Reflections(R-Work) 4760
    R-Factor(R-Work) 0.1312
    R-Factor(R-Free) 0.2082
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.839
    Shell Resolution(Low) 8.956
    Number of Reflections(R-Free) 255
    Number of Reflections(R-Work) 4698
    R-Factor(R-Work) 0.1351
    R-Factor(R-Free) 0.1789
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.956
    Shell Resolution(Low) 11.2192
    Number of Reflections(R-Free) 253
    Number of Reflections(R-Work) 4701
    R-Factor(R-Work) 0.1419
    R-Factor(R-Free) 0.1906
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 11.2192
    Shell Resolution(Low) 34.5625
    Number of Reflections(R-Free) 247
    Number of Reflections(R-Work) 4512
    R-Factor(R-Work) 0.2042
    R-Factor(R-Free) 0.247
    Percent Reflections(Observed) 85.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 20.366
    f_plane_restr 0.01
    f_chiral_restr 0.094
    f_angle_d 1.698
    f_bond_d 0.014
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 19088
    Nucleic Acid Atoms 32507
    Heterogen Atoms 309
    Solvent Atoms 385
     
     
  •   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