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X-RAY DIFFRACTION
Materials and Methods page
4DUY
  •   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 = 175.89 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) 3.39
    Resolution(Low) 35
    Number Reflections(All) 192883
    Number Reflections(Observed) 192883
    Percent Possible(Observed) 97.5
    R Merge I(Observed) 0.064
    Redundancy 3.1
     
    High Resolution Shell Details
    Resolution(High) 3.386
    Resolution(Low) 3.52
    Percent Possible(All) 98.2
    R Merge I(Observed) 0.647
    Redundancy 3.0
    Number Unique Reflections(All) 19239
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 3.386
    Resolution(Low) 34.872
    Cut-off Sigma(F) 1.34
    Number of Reflections(all) 192822
    Number of Reflections(Observed) 192822
    Number of Reflections(R-Free) 9696
    Percent Reflections(Observed) 97.01
    R-Factor(Observed) 0.1612
    R-Work 0.159
    R-Free 0.202
    R-Free Selection Details FROM PDB ENTRY 2VQE
     
    Temperature Factor Modeling
    Mean Isotropic B Value 141.937
    Anisotropic B[1][1] -3.7886
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -3.7886
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 11.9917
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.386
    Shell Resolution(Low) 3.4246
    Number of Reflections(R-Free) 289
    Number of Reflections(R-Work) 5152
    R-Factor(R-Work) 0.2886
    R-Factor(R-Free) 0.3161
    Percent Reflections(Observed) 83.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4246
    Shell Resolution(Low) 3.4649
    Number of Reflections(R-Free) 329
    Number of Reflections(R-Work) 6109
    R-Factor(R-Work) 0.2853
    R-Factor(R-Free) 0.3308
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4649
    Shell Resolution(Low) 3.5071
    Number of Reflections(R-Free) 323
    Number of Reflections(R-Work) 6094
    R-Factor(R-Work) 0.2786
    R-Factor(R-Free) 0.3538
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5071
    Shell Resolution(Low) 3.5514
    Number of Reflections(R-Free) 363
    Number of Reflections(R-Work) 6066
    R-Factor(R-Work) 0.2654
    R-Factor(R-Free) 0.3063
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5514
    Shell Resolution(Low) 3.5981
    Number of Reflections(R-Free) 339
    Number of Reflections(R-Work) 6162
    R-Factor(R-Work) 0.2461
    R-Factor(R-Free) 0.2959
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5981
    Shell Resolution(Low) 3.6474
    Number of Reflections(R-Free) 310
    Number of Reflections(R-Work) 6121
    R-Factor(R-Work) 0.234
    R-Factor(R-Free) 0.2995
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6474
    Shell Resolution(Low) 3.6994
    Number of Reflections(R-Free) 345
    Number of Reflections(R-Work) 6097
    R-Factor(R-Work) 0.2187
    R-Factor(R-Free) 0.2444
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6994
    Shell Resolution(Low) 3.7546
    Number of Reflections(R-Free) 342
    Number of Reflections(R-Work) 6169
    R-Factor(R-Work) 0.2062
    R-Factor(R-Free) 0.2428
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7546
    Shell Resolution(Low) 3.8132
    Number of Reflections(R-Free) 307
    Number of Reflections(R-Work) 6130
    R-Factor(R-Work) 0.19
    R-Factor(R-Free) 0.2195
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8132
    Shell Resolution(Low) 3.8756
    Number of Reflections(R-Free) 309
    Number of Reflections(R-Work) 6158
    R-Factor(R-Work) 0.1792
    R-Factor(R-Free) 0.2307
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8756
    Shell Resolution(Low) 3.9423
    Number of Reflections(R-Free) 340
    Number of Reflections(R-Work) 6150
    R-Factor(R-Work) 0.1816
    R-Factor(R-Free) 0.2366
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9423
    Shell Resolution(Low) 4.0139
    Number of Reflections(R-Free) 308
    Number of Reflections(R-Work) 6180
    R-Factor(R-Work) 0.1759
    R-Factor(R-Free) 0.2132
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0139
    Shell Resolution(Low) 4.091
    Number of Reflections(R-Free) 354
    Number of Reflections(R-Work) 6154
    R-Factor(R-Work) 0.1753
    R-Factor(R-Free) 0.2307
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.091
    Shell Resolution(Low) 4.1744
    Number of Reflections(R-Free) 323
    Number of Reflections(R-Work) 6168
    R-Factor(R-Work) 0.1569
    R-Factor(R-Free) 0.2074
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1744
    Shell Resolution(Low) 4.265
    Number of Reflections(R-Free) 308
    Number of Reflections(R-Work) 6204
    R-Factor(R-Work) 0.1519
    R-Factor(R-Free) 0.2159
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.265
    Shell Resolution(Low) 4.364
    Number of Reflections(R-Free) 347
    Number of Reflections(R-Work) 6141
    R-Factor(R-Work) 0.1443
    R-Factor(R-Free) 0.2007
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.364
    Shell Resolution(Low) 4.473
    Number of Reflections(R-Free) 335
    Number of Reflections(R-Work) 6201
    R-Factor(R-Work) 0.1392
    R-Factor(R-Free) 0.1805
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.473
    Shell Resolution(Low) 4.5936
    Number of Reflections(R-Free) 339
    Number of Reflections(R-Work) 6162
    R-Factor(R-Work) 0.1333
    R-Factor(R-Free) 0.1803
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5936
    Shell Resolution(Low) 4.7285
    Number of Reflections(R-Free) 302
    Number of Reflections(R-Work) 6222
    R-Factor(R-Work) 0.1311
    R-Factor(R-Free) 0.1802
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7285
    Shell Resolution(Low) 4.8807
    Number of Reflections(R-Free) 301
    Number of Reflections(R-Work) 6245
    R-Factor(R-Work) 0.1289
    R-Factor(R-Free) 0.1781
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8807
    Shell Resolution(Low) 5.0547
    Number of Reflections(R-Free) 355
    Number of Reflections(R-Work) 6124
    R-Factor(R-Work) 0.1259
    R-Factor(R-Free) 0.1686
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0547
    Shell Resolution(Low) 5.2564
    Number of Reflections(R-Free) 286
    Number of Reflections(R-Work) 6206
    R-Factor(R-Work) 0.1189
    R-Factor(R-Free) 0.1631
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2564
    Shell Resolution(Low) 5.4948
    Number of Reflections(R-Free) 317
    Number of Reflections(R-Work) 6203
    R-Factor(R-Work) 0.1222
    R-Factor(R-Free) 0.1731
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.4948
    Shell Resolution(Low) 5.7832
    Number of Reflections(R-Free) 348
    Number of Reflections(R-Work) 6133
    R-Factor(R-Work) 0.122
    R-Factor(R-Free) 0.177
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.7832
    Shell Resolution(Low) 6.1437
    Number of Reflections(R-Free) 289
    Number of Reflections(R-Work) 6200
    R-Factor(R-Work) 0.1305
    R-Factor(R-Free) 0.1807
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.1437
    Shell Resolution(Low) 6.6151
    Number of Reflections(R-Free) 309
    Number of Reflections(R-Work) 6145
    R-Factor(R-Work) 0.1339
    R-Factor(R-Free) 0.1729
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.6151
    Shell Resolution(Low) 7.2754
    Number of Reflections(R-Free) 328
    Number of Reflections(R-Work) 6130
    R-Factor(R-Work) 0.1359
    R-Factor(R-Free) 0.1906
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.2754
    Shell Resolution(Low) 8.3156
    Number of Reflections(R-Free) 298
    Number of Reflections(R-Work) 6108
    R-Factor(R-Work) 0.1378
    R-Factor(R-Free) 0.1799
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.3156
    Shell Resolution(Low) 10.4301
    Number of Reflections(R-Free) 346
    Number of Reflections(R-Work) 6026
    R-Factor(R-Work) 0.1525
    R-Factor(R-Free) 0.1745
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 10.4301
    Shell Resolution(Low) 34.8735
    Number of Reflections(R-Free) 307
    Number of Reflections(R-Work) 5766
    R-Factor(R-Work) 0.1946
    R-Factor(R-Free) 0.2146
    Percent Reflections(Observed) 86.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 18.075
    f_plane_restr 0.005
    f_chiral_restr 0.067
    f_angle_d 0.934
    f_bond_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 19088
    Nucleic Acid Atoms 32507
    Heterogen Atoms 314
    Solvent Atoms 538
     
     
  •   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