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X-RAY DIFFRACTION
Materials and Methods page
4GYQ
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 6.5
    Temperature 289.0
    Details 0.2 M magnesium chloride, 0.1 M Bis-Tris pH 6.5, 25 %(w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 69.14 α = 90
    b = 74.22 β = 90.11
    c = 76.6 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315r
    Details mirrors
    Collection Date 2011-10-30
     
    Diffraction Radiation
    Monochromator double crystal monochromator
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 19-ID
    Wavelength List 0.97929
    Site APS
    Beamline 19-ID
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.35
    Resolution(Low) 50
    Number Reflections(All) 162811
    Number Reflections(Observed) 162811
    Percent Possible(Observed) 96.5
    B(Isotropic) From Wilson Plot 14.23
    Redundancy 7.2
     
    High Resolution Shell Details
    Resolution(High) 1.35
    Resolution(Low) 1.36
    Percent Possible(All) 69.1
    Mean I Over Sigma(Observed) 2.0
    R-Sym I(Observed) 0.582
    Redundancy 4.0
    Number Unique Reflections(All) 5774
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MIR
    reflnsShellList 1.351
    Resolution(Low) 34.036
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 162771
    Number of Reflections(Observed) 162771
    Number of Reflections(R-Free) 8178
    Percent Reflections(Observed) 96.21
    R-Factor(All) 0.145
    R-Factor(Observed) 0.145
    R-Work 0.143
    R-Free 0.1805
    R-Free Selection Details random, 5%
     
    Temperature Factor Modeling
    Isotropic Thermal Model mixed
    Mean Isotropic B Value 19.9
    Anisotropic B[1][1] -0.1296
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -1.4325
    Anisotropic B[2][2] -1.3972
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 1.5268
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.351
    Shell Resolution(Low) 1.3663
    Number of Reflections(Observed) 3526
    Number of Reflections(R-Free) 170
    Number of Reflections(R-Work) 3356
    R-Factor(R-Work) 0.2968
    R-Factor(R-Free) 0.3564
    Percent Reflections(Observed) 63.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3663
    Shell Resolution(Low) 1.3824
    Number of Reflections(Observed) 4096
    Number of Reflections(R-Free) 231
    Number of Reflections(R-Work) 3865
    R-Factor(R-Work) 0.2796
    R-Factor(R-Free) 0.3079
    Percent Reflections(Observed) 73.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3824
    Shell Resolution(Low) 1.3993
    Number of Reflections(Observed) 4488
    Number of Reflections(R-Free) 249
    Number of Reflections(R-Work) 4239
    R-Factor(R-Work) 0.2492
    R-Factor(R-Free) 0.3094
    Percent Reflections(Observed) 80.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3993
    Shell Resolution(Low) 1.417
    Number of Reflections(Observed) 4837
    Number of Reflections(R-Free) 287
    Number of Reflections(R-Work) 4550
    R-Factor(R-Work) 0.2232
    R-Factor(R-Free) 0.2857
    Percent Reflections(Observed) 86.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.417
    Shell Resolution(Low) 1.4356
    Number of Reflections(Observed) 5113
    Number of Reflections(R-Free) 231
    Number of Reflections(R-Work) 4882
    R-Factor(R-Work) 0.2095
    R-Factor(R-Free) 0.2432
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4356
    Shell Resolution(Low) 1.4553
    Number of Reflections(Observed) 5358
    Number of Reflections(R-Free) 276
    Number of Reflections(R-Work) 5082
    R-Factor(R-Work) 0.1958
    R-Factor(R-Free) 0.2717
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4553
    Shell Resolution(Low) 1.4761
    Number of Reflections(Observed) 5532
    Number of Reflections(R-Free) 298
    Number of Reflections(R-Work) 5234
    R-Factor(R-Work) 0.1826
    R-Factor(R-Free) 0.2403
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4761
    Shell Resolution(Low) 1.4981
    Number of Reflections(Observed) 5572
    Number of Reflections(R-Free) 245
    Number of Reflections(R-Work) 5327
    R-Factor(R-Work) 0.1559
    R-Factor(R-Free) 0.2196
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4981
    Shell Resolution(Low) 1.5215
    Number of Reflections(Observed) 5620
    Number of Reflections(R-Free) 273
    Number of Reflections(R-Work) 5347
    R-Factor(R-Work) 0.1399
    R-Factor(R-Free) 0.2103
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5215
    Shell Resolution(Low) 1.5465
    Number of Reflections(Observed) 5663
    Number of Reflections(R-Free) 278
    Number of Reflections(R-Work) 5385
    R-Factor(R-Work) 0.1371
    R-Factor(R-Free) 0.1788
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5465
    Shell Resolution(Low) 1.5731
    Number of Reflections(Observed) 5621
    Number of Reflections(R-Free) 265
    Number of Reflections(R-Work) 5356
    R-Factor(R-Work) 0.1324
    R-Factor(R-Free) 0.2022
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5731
    Shell Resolution(Low) 1.6017
    Number of Reflections(Observed) 5600
    Number of Reflections(R-Free) 276
    Number of Reflections(R-Work) 5324
    R-Factor(R-Work) 0.1341
    R-Factor(R-Free) 0.1809
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6017
    Shell Resolution(Low) 1.6325
    Number of Reflections(Observed) 5640
    Number of Reflections(R-Free) 257
    Number of Reflections(R-Work) 5383
    R-Factor(R-Work) 0.1171
    R-Factor(R-Free) 0.2058
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6325
    Shell Resolution(Low) 1.6659
    Number of Reflections(Observed) 5662
    Number of Reflections(R-Free) 277
    Number of Reflections(R-Work) 5385
    R-Factor(R-Work) 0.1103
    R-Factor(R-Free) 0.1669
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6659
    Shell Resolution(Low) 1.7021
    Number of Reflections(Observed) 5572
    Number of Reflections(R-Free) 272
    Number of Reflections(R-Work) 5300
    R-Factor(R-Work) 0.108
    R-Factor(R-Free) 0.164
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7021
    Shell Resolution(Low) 1.7417
    Number of Reflections(Observed) 5667
    Number of Reflections(R-Free) 283
    Number of Reflections(R-Work) 5384
    R-Factor(R-Work) 0.11
    R-Factor(R-Free) 0.1668
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7417
    Shell Resolution(Low) 1.7852
    Number of Reflections(Observed) 5601
    Number of Reflections(R-Free) 253
    Number of Reflections(R-Work) 5348
    R-Factor(R-Work) 0.1181
    R-Factor(R-Free) 0.1666
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7852
    Shell Resolution(Low) 1.8335
    Number of Reflections(Observed) 5623
    Number of Reflections(R-Free) 281
    Number of Reflections(R-Work) 5342
    R-Factor(R-Work) 0.1243
    R-Factor(R-Free) 0.1691
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8335
    Shell Resolution(Low) 1.8874
    Number of Reflections(Observed) 5619
    Number of Reflections(R-Free) 296
    Number of Reflections(R-Work) 5323
    R-Factor(R-Work) 0.1225
    R-Factor(R-Free) 0.1907
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8874
    Shell Resolution(Low) 1.9484
    Number of Reflections(Observed) 5668
    Number of Reflections(R-Free) 277
    Number of Reflections(R-Work) 5391
    R-Factor(R-Work) 0.1246
    R-Factor(R-Free) 0.1736
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9484
    Shell Resolution(Low) 2.018
    Number of Reflections(Observed) 5651
    Number of Reflections(R-Free) 283
    Number of Reflections(R-Work) 5368
    R-Factor(R-Work) 0.1303
    R-Factor(R-Free) 0.1624
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.018
    Shell Resolution(Low) 2.0988
    Number of Reflections(Observed) 5623
    Number of Reflections(R-Free) 260
    Number of Reflections(R-Work) 5363
    R-Factor(R-Work) 0.1355
    R-Factor(R-Free) 0.1746
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0988
    Shell Resolution(Low) 2.1943
    Number of Reflections(Observed) 5653
    Number of Reflections(R-Free) 292
    Number of Reflections(R-Work) 5361
    R-Factor(R-Work) 0.1362
    R-Factor(R-Free) 0.1771
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1943
    Shell Resolution(Low) 2.3099
    Number of Reflections(Observed) 5677
    Number of Reflections(R-Free) 301
    Number of Reflections(R-Work) 5376
    R-Factor(R-Work) 0.1329
    R-Factor(R-Free) 0.1575
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3099
    Shell Resolution(Low) 2.4546
    Number of Reflections(Observed) 5628
    Number of Reflections(R-Free) 256
    Number of Reflections(R-Work) 5372
    R-Factor(R-Work) 0.1394
    R-Factor(R-Free) 0.1702
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4546
    Shell Resolution(Low) 2.6441
    Number of Reflections(Observed) 5683
    Number of Reflections(R-Free) 307
    Number of Reflections(R-Work) 5376
    R-Factor(R-Work) 0.1381
    R-Factor(R-Free) 0.176
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6441
    Shell Resolution(Low) 2.91
    Number of Reflections(Observed) 5642
    Number of Reflections(R-Free) 305
    Number of Reflections(R-Work) 5337
    R-Factor(R-Work) 0.1467
    R-Factor(R-Free) 0.1673
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.91
    Shell Resolution(Low) 3.3308
    Number of Reflections(Observed) 5696
    Number of Reflections(R-Free) 315
    Number of Reflections(R-Work) 5381
    R-Factor(R-Work) 0.1511
    R-Factor(R-Free) 0.1934
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3308
    Shell Resolution(Low) 4.1953
    Number of Reflections(Observed) 5677
    Number of Reflections(R-Free) 306
    Number of Reflections(R-Work) 5371
    R-Factor(R-Work) 0.1386
    R-Factor(R-Free) 0.1519
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1953
    Shell Resolution(Low) 34.0464
    Number of Reflections(Observed) 5763
    Number of Reflections(R-Free) 278
    Number of Reflections(R-Work) 5485
    R-Factor(R-Work) 0.1583
    R-Factor(R-Free) 0.1805
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.006
    f_chiral_restr 0.08
    f_dihedral_angle_d 12.562
    f_angle_d 1.147
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 6937
    Nucleic Acid Atoms 0
    Heterogen Atoms 13
    Solvent Atoms 1049
     
     
  •   Software and Computing Hide
    Computing
    Data Collection sBCCOLLECT, HKL3000
    Data Reduction (intensity integration) HKL-3000
    Data Reduction (data scaling) HKL-3000
    Structure Solution HKL3000, Molrep
    Structure Refinement PHENIX (phenix.refine: 1.7.3_920)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7.3_920)
    model building Molrep
    model building HKL3000
    data collection HKL3000
    data collection sBCCOLLECT