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X-RAY DIFFRACTION
Materials and Methods page
4GG1
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 8.5
    Temperature 298.0
    Details 100 mM Tris pH 8.5, 22% v/v PEG 400, 150 mM CaCl2, 0.5% v/v MPD [2-METHYL-2,4-PENTANEDIOL], VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 81.43 α = 90
    b = 95.6 β = 90
    c = 137.01 γ = 90
     
    Space Group
    Space Group Name:    I 2 2 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 300 mm CCD
    Collection Date 2011-07-07
     
    Diffraction Radiation
    Monochromator double crystal monochromator
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 23-ID-B
    Wavelength List 1.033
    Site APS
    Beamline 23-ID-B
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 1.34
    Resolution(High) 1.07
    Resolution(Low) 45.97
    Number Reflections(Observed) 220519
    Percent Possible(Observed) 94.1
     
    High Resolution Shell Details
    Resolution(High) 1.07
    Resolution(Low) 1.11
    Percent Possible(All) 61.1
    Mean I Over Sigma(Observed) 1.34
    Redundancy 2.6
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.069
    Resolution(Low) 45.965
    Cut-off Sigma(F) 1.34
    Number of Reflections(Observed) 220519
    Number of Reflections(R-Free) 11067
    Percent Reflections(Observed) 94.1
    R-Factor(Observed) 0.1399
    R-Work 0.139
    R-Free 0.156
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Anisotropic B[1][1] 2.4982
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -1.0391
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -1.459
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.0687
    Shell Resolution(Low) 1.0808
    Number of Reflections(R-Free) 211
    Number of Reflections(R-Work) 3779
    R-Factor(R-Work) 0.3171
    R-Factor(R-Free) 0.3422
    Percent Reflections(Observed) 51.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.0808
    Shell Resolution(Low) 1.0935
    Number of Reflections(R-Free) 226
    Number of Reflections(R-Work) 4499
    R-Factor(R-Work) 0.2736
    R-Factor(R-Free) 0.2949
    Percent Reflections(Observed) 61.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.0935
    Shell Resolution(Low) 1.1069
    Number of Reflections(R-Free) 303
    Number of Reflections(R-Work) 5055
    R-Factor(R-Work) 0.25
    R-Factor(R-Free) 0.2655
    Percent Reflections(Observed) 69.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.1069
    Shell Resolution(Low) 1.1209
    Number of Reflections(R-Free) 301
    Number of Reflections(R-Work) 5638
    R-Factor(R-Work) 0.2187
    R-Factor(R-Free) 0.254
    Percent Reflections(Observed) 76.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.1209
    Shell Resolution(Low) 1.1356
    Number of Reflections(R-Free) 311
    Number of Reflections(R-Work) 6114
    R-Factor(R-Work) 0.207
    R-Factor(R-Free) 0.2319
    Percent Reflections(Observed) 83.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.1356
    Shell Resolution(Low) 1.1512
    Number of Reflections(R-Free) 367
    Number of Reflections(R-Work) 6635
    R-Factor(R-Work) 0.1842
    R-Factor(R-Free) 0.2099
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.1512
    Shell Resolution(Low) 1.1676
    Number of Reflections(R-Free) 362
    Number of Reflections(R-Work) 7021
    R-Factor(R-Work) 0.1707
    R-Factor(R-Free) 0.1809
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.1676
    Shell Resolution(Low) 1.1851
    Number of Reflections(R-Free) 365
    Number of Reflections(R-Work) 7270
    R-Factor(R-Work) 0.1524
    R-Factor(R-Free) 0.1695
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.1851
    Shell Resolution(Low) 1.2036
    Number of Reflections(R-Free) 369
    Number of Reflections(R-Work) 7358
    R-Factor(R-Work) 0.1422
    R-Factor(R-Free) 0.1733
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.2036
    Shell Resolution(Low) 1.2233
    Number of Reflections(R-Free) 371
    Number of Reflections(R-Work) 7377
    R-Factor(R-Work) 0.1361
    R-Factor(R-Free) 0.1589
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.2233
    Shell Resolution(Low) 1.2444
    Number of Reflections(R-Free) 361
    Number of Reflections(R-Work) 7355
    R-Factor(R-Work) 0.1363
    R-Factor(R-Free) 0.1532
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.2444
    Shell Resolution(Low) 1.2671
    Number of Reflections(R-Free) 389
    Number of Reflections(R-Work) 7324
    R-Factor(R-Work) 0.1286
    R-Factor(R-Free) 0.1606
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.2671
    Shell Resolution(Low) 1.2914
    Number of Reflections(R-Free) 395
    Number of Reflections(R-Work) 7404
    R-Factor(R-Work) 0.1259
    R-Factor(R-Free) 0.1543
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.2914
    Shell Resolution(Low) 1.3178
    Number of Reflections(R-Free) 391
    Number of Reflections(R-Work) 7348
    R-Factor(R-Work) 0.1241
    R-Factor(R-Free) 0.1399
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3178
    Shell Resolution(Low) 1.3464
    Number of Reflections(R-Free) 384
    Number of Reflections(R-Work) 7413
    R-Factor(R-Work) 0.1211
    R-Factor(R-Free) 0.1434
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3464
    Shell Resolution(Low) 1.3778
    Number of Reflections(R-Free) 374
    Number of Reflections(R-Work) 7339
    R-Factor(R-Work) 0.1181
    R-Factor(R-Free) 0.1346
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3778
    Shell Resolution(Low) 1.4122
    Number of Reflections(R-Free) 384
    Number of Reflections(R-Work) 7421
    R-Factor(R-Work) 0.1222
    R-Factor(R-Free) 0.1338
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4122
    Shell Resolution(Low) 1.4504
    Number of Reflections(R-Free) 378
    Number of Reflections(R-Work) 7460
    R-Factor(R-Work) 0.1177
    R-Factor(R-Free) 0.1437
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4504
    Shell Resolution(Low) 1.4931
    Number of Reflections(R-Free) 386
    Number of Reflections(R-Work) 7371
    R-Factor(R-Work) 0.1144
    R-Factor(R-Free) 0.1504
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4931
    Shell Resolution(Low) 1.5413
    Number of Reflections(R-Free) 383
    Number of Reflections(R-Work) 7393
    R-Factor(R-Work) 0.1102
    R-Factor(R-Free) 0.1382
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5413
    Shell Resolution(Low) 1.5964
    Number of Reflections(R-Free) 394
    Number of Reflections(R-Work) 7437
    R-Factor(R-Work) 0.1101
    R-Factor(R-Free) 0.1242
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5964
    Shell Resolution(Low) 1.6603
    Number of Reflections(R-Free) 404
    Number of Reflections(R-Work) 7429
    R-Factor(R-Work) 0.111
    R-Factor(R-Free) 0.135
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6603
    Shell Resolution(Low) 1.7359
    Number of Reflections(R-Free) 394
    Number of Reflections(R-Work) 7391
    R-Factor(R-Work) 0.1141
    R-Factor(R-Free) 0.1399
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7359
    Shell Resolution(Low) 1.8274
    Number of Reflections(R-Free) 382
    Number of Reflections(R-Work) 7458
    R-Factor(R-Work) 0.1212
    R-Factor(R-Free) 0.1487
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8274
    Shell Resolution(Low) 1.9419
    Number of Reflections(R-Free) 422
    Number of Reflections(R-Work) 7421
    R-Factor(R-Work) 0.1306
    R-Factor(R-Free) 0.1412
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9419
    Shell Resolution(Low) 2.0918
    Number of Reflections(R-Free) 384
    Number of Reflections(R-Work) 7464
    R-Factor(R-Work) 0.1322
    R-Factor(R-Free) 0.1407
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0918
    Shell Resolution(Low) 2.3023
    Number of Reflections(R-Free) 419
    Number of Reflections(R-Work) 7456
    R-Factor(R-Work) 0.134
    R-Factor(R-Free) 0.1559
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3023
    Shell Resolution(Low) 2.6354
    Number of Reflections(R-Free) 394
    Number of Reflections(R-Work) 7522
    R-Factor(R-Work) 0.1418
    R-Factor(R-Free) 0.1484
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6354
    Shell Resolution(Low) 3.3202
    Number of Reflections(R-Free) 426
    Number of Reflections(R-Work) 7546
    R-Factor(R-Work) 0.1492
    R-Factor(R-Free) 0.1618
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3202
    Shell Resolution(Low) 46.008
    Number of Reflections(R-Free) 437
    Number of Reflections(R-Work) 7754
    R-Factor(R-Work) 0.1491
    R-Factor(R-Free) 0.1561
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.011
    f_chiral_restr 0.1
    f_dihedral_angle_d 13.237
    f_angle_d 1.648
    f_bond_d 0.015
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3940
    Nucleic Acid Atoms 0
    Heterogen Atoms 42
    Solvent Atoms 575
     
     
  •   Software and Computing Hide
    Computing
    Data Collection BluIce
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHENIX
    Structure Refinement PHENIX (phenix.refine: 1.7.3_928)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7.3_928)
    model building PHENIX
    data collection BluIce