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X-RAY DIFFRACTION
Materials and Methods page
4DR3
  •   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 = 404.04 α = 90
    b = 404.04 β = 90
    c = 173.53 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 2011-11-07
     
    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) 3.35
    Resolution(Low) 35
    Number Reflections(All) 200934
    Number Reflections(Observed) 200934
    Percent Possible(Observed) 98.3
    R Merge I(Observed) 0.062
    Redundancy 3.3
     
    High Resolution Shell Details
    Resolution(High) 3.348
    Resolution(Low) 3.47
    Percent Possible(All) 99.0
    R Merge I(Observed) 0.634
    Redundancy 3.3
    Number Unique Reflections(All) 19994
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 3.348
    Resolution(Low) 34.552
    Cut-off Sigma(F) 1.34
    Number of Reflections(all) 200881
    Number of Reflections(Observed) 200881
    Number of Reflections(R-Free) 10115
    Percent Reflections(Observed) 98.32
    R-Factor(Observed) 0.1695
    R-Work 0.1676
    R-Free 0.2063
    R-Free Selection Details FROM PDB ENTRY 2VQE
     
    Temperature Factor Modeling
    Mean Isotropic B Value 147.169
    Anisotropic B[1][1] -8.699
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -8.699
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 17.398
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.348
    Shell Resolution(Low) 3.3864
    Number of Reflections(R-Free) 330
    Number of Reflections(R-Work) 6238
    R-Factor(R-Work) 0.2899
    R-Factor(R-Free) 0.3452
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3864
    Shell Resolution(Low) 3.4262
    Number of Reflections(R-Free) 360
    Number of Reflections(R-Work) 6294
    R-Factor(R-Work) 0.2866
    R-Factor(R-Free) 0.35
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4262
    Shell Resolution(Low) 3.4679
    Number of Reflections(R-Free) 340
    Number of Reflections(R-Work) 6342
    R-Factor(R-Work) 0.2692
    R-Factor(R-Free) 0.3022
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4679
    Shell Resolution(Low) 3.5118
    Number of Reflections(R-Free) 371
    Number of Reflections(R-Work) 6352
    R-Factor(R-Work) 0.2569
    R-Factor(R-Free) 0.3028
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5118
    Shell Resolution(Low) 3.558
    Number of Reflections(R-Free) 337
    Number of Reflections(R-Work) 6334
    R-Factor(R-Work) 0.2442
    R-Factor(R-Free) 0.2795
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.558
    Shell Resolution(Low) 3.6066
    Number of Reflections(R-Free) 353
    Number of Reflections(R-Work) 6342
    R-Factor(R-Work) 0.2304
    R-Factor(R-Free) 0.2666
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6066
    Shell Resolution(Low) 3.6581
    Number of Reflections(R-Free) 343
    Number of Reflections(R-Work) 6363
    R-Factor(R-Work) 0.2188
    R-Factor(R-Free) 0.2532
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6581
    Shell Resolution(Low) 3.7127
    Number of Reflections(R-Free) 350
    Number of Reflections(R-Work) 6341
    R-Factor(R-Work) 0.2113
    R-Factor(R-Free) 0.2605
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7127
    Shell Resolution(Low) 3.7706
    Number of Reflections(R-Free) 363
    Number of Reflections(R-Work) 6340
    R-Factor(R-Work) 0.1971
    R-Factor(R-Free) 0.2287
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7706
    Shell Resolution(Low) 3.8323
    Number of Reflections(R-Free) 292
    Number of Reflections(R-Work) 6445
    R-Factor(R-Work) 0.1953
    R-Factor(R-Free) 0.2412
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8323
    Shell Resolution(Low) 3.8983
    Number of Reflections(R-Free) 338
    Number of Reflections(R-Work) 6370
    R-Factor(R-Work) 0.1832
    R-Factor(R-Free) 0.2114
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8983
    Shell Resolution(Low) 3.9691
    Number of Reflections(R-Free) 337
    Number of Reflections(R-Work) 6359
    R-Factor(R-Work) 0.1728
    R-Factor(R-Free) 0.2106
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9691
    Shell Resolution(Low) 4.0454
    Number of Reflections(R-Free) 348
    Number of Reflections(R-Work) 6362
    R-Factor(R-Work) 0.1689
    R-Factor(R-Free) 0.2102
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0454
    Shell Resolution(Low) 4.1278
    Number of Reflections(R-Free) 369
    Number of Reflections(R-Work) 6386
    R-Factor(R-Work) 0.17
    R-Factor(R-Free) 0.216
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1278
    Shell Resolution(Low) 4.2174
    Number of Reflections(R-Free) 321
    Number of Reflections(R-Work) 6408
    R-Factor(R-Work) 0.1547
    R-Factor(R-Free) 0.1972
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2174
    Shell Resolution(Low) 4.3153
    Number of Reflections(R-Free) 328
    Number of Reflections(R-Work) 6423
    R-Factor(R-Work) 0.1551
    R-Factor(R-Free) 0.223
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3153
    Shell Resolution(Low) 4.423
    Number of Reflections(R-Free) 346
    Number of Reflections(R-Work) 6387
    R-Factor(R-Work) 0.1568
    R-Factor(R-Free) 0.195
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.423
    Shell Resolution(Low) 4.5424
    Number of Reflections(R-Free) 369
    Number of Reflections(R-Work) 6395
    R-Factor(R-Work) 0.1495
    R-Factor(R-Free) 0.1868
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5424
    Shell Resolution(Low) 4.6757
    Number of Reflections(R-Free) 326
    Number of Reflections(R-Work) 6445
    R-Factor(R-Work) 0.1448
    R-Factor(R-Free) 0.1883
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6757
    Shell Resolution(Low) 4.8263
    Number of Reflections(R-Free) 302
    Number of Reflections(R-Work) 6402
    R-Factor(R-Work) 0.1379
    R-Factor(R-Free) 0.1633
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8263
    Shell Resolution(Low) 4.9983
    Number of Reflections(R-Free) 353
    Number of Reflections(R-Work) 6406
    R-Factor(R-Work) 0.129
    R-Factor(R-Free) 0.174
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9983
    Shell Resolution(Low) 5.1978
    Number of Reflections(R-Free) 316
    Number of Reflections(R-Work) 6444
    R-Factor(R-Work) 0.1335
    R-Factor(R-Free) 0.1826
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1978
    Shell Resolution(Low) 5.4334
    Number of Reflections(R-Free) 323
    Number of Reflections(R-Work) 6442
    R-Factor(R-Work) 0.1346
    R-Factor(R-Free) 0.1853
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.4334
    Shell Resolution(Low) 5.7187
    Number of Reflections(R-Free) 341
    Number of Reflections(R-Work) 6380
    R-Factor(R-Work) 0.1325
    R-Factor(R-Free) 0.1727
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.7187
    Shell Resolution(Low) 6.0752
    Number of Reflections(R-Free) 326
    Number of Reflections(R-Work) 6405
    R-Factor(R-Work) 0.1415
    R-Factor(R-Free) 0.1871
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.0752
    Shell Resolution(Low) 6.5413
    Number of Reflections(R-Free) 307
    Number of Reflections(R-Work) 6411
    R-Factor(R-Work) 0.148
    R-Factor(R-Free) 0.181
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.5413
    Shell Resolution(Low) 7.1943
    Number of Reflections(R-Free) 341
    Number of Reflections(R-Work) 6398
    R-Factor(R-Work) 0.1441
    R-Factor(R-Free) 0.1943
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.1943
    Shell Resolution(Low) 8.223
    Number of Reflections(R-Free) 315
    Number of Reflections(R-Work) 6347
    R-Factor(R-Work) 0.1451
    R-Factor(R-Free) 0.1985
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.223
    Shell Resolution(Low) 10.3142
    Number of Reflections(R-Free) 359
    Number of Reflections(R-Work) 6260
    R-Factor(R-Work) 0.163
    R-Factor(R-Free) 0.1857
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 10.3142
    Shell Resolution(Low) 34.5537
    Number of Reflections(R-Free) 311
    Number of Reflections(R-Work) 5945
    R-Factor(R-Work) 0.2039
    R-Factor(R-Free) 0.2145
    Percent Reflections(Observed) 86.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 17.902
    f_plane_restr 0.005
    f_chiral_restr 0.068
    f_angle_d 0.964
    f_bond_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 19088
    Nucleic Acid Atoms 32507
    Heterogen Atoms 306
    Solvent Atoms 263
     
     
  •   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