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X-RAY DIFFRACTION
Materials and Methods page
4DR1
  •   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 = 403.04 α = 90
    b = 403.04 β = 90
    c = 174.36 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) 3.6
    Resolution(Low) 35
    Number Reflections(All) 163468
    Number Reflections(Observed) 163468
    Percent Possible(Observed) 99.2
    R Merge I(Observed) 0.085
    Redundancy 4.8
     
    High Resolution Shell Details
    Resolution(High) 3.6
    Resolution(Low) 3.73
    Percent Possible(All) 99.2
    R Merge I(Observed) 0.923
    Redundancy 4.8
    Number Unique Reflections(All) 16146
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 3.6
    Resolution(Low) 34.644
    Cut-off Sigma(F) 1.33
    Number of Reflections(all) 163397
    Number of Reflections(Observed) 163397
    Number of Reflections(R-Free) 8155
    Percent Reflections(Observed) 99.21
    R-Factor(Observed) 0.1594
    R-Work 0.1568
    R-Free 0.2066
    R-Free Selection Details FROM PDB ENTRY 2VQE
     
    Temperature Factor Modeling
    Mean Isotropic B Value 167.854
    Anisotropic B[1][1] -4.2438
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -4.2438
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 8.4876
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6
    Shell Resolution(Low) 3.6413
    Number of Reflections(R-Free) 252
    Number of Reflections(R-Work) 5075
    R-Factor(R-Work) 0.2799
    R-Factor(R-Free) 0.3241
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6413
    Shell Resolution(Low) 3.6841
    Number of Reflections(R-Free) 296
    Number of Reflections(R-Work) 5116
    R-Factor(R-Work) 0.2627
    R-Factor(R-Free) 0.2983
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6841
    Shell Resolution(Low) 3.729
    Number of Reflections(R-Free) 280
    Number of Reflections(R-Work) 5111
    R-Factor(R-Work) 0.2535
    R-Factor(R-Free) 0.3063
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.729
    Shell Resolution(Low) 3.7761
    Number of Reflections(R-Free) 302
    Number of Reflections(R-Work) 5133
    R-Factor(R-Work) 0.2359
    R-Factor(R-Free) 0.2841
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7761
    Shell Resolution(Low) 3.8258
    Number of Reflections(R-Free) 221
    Number of Reflections(R-Work) 5130
    R-Factor(R-Work) 0.2203
    R-Factor(R-Free) 0.2778
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8258
    Shell Resolution(Low) 3.8781
    Number of Reflections(R-Free) 275
    Number of Reflections(R-Work) 5143
    R-Factor(R-Work) 0.2101
    R-Factor(R-Free) 0.2549
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8781
    Shell Resolution(Low) 3.9334
    Number of Reflections(R-Free) 267
    Number of Reflections(R-Work) 5153
    R-Factor(R-Work) 0.2002
    R-Factor(R-Free) 0.2489
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9334
    Shell Resolution(Low) 3.9921
    Number of Reflections(R-Free) 270
    Number of Reflections(R-Work) 5142
    R-Factor(R-Work) 0.1928
    R-Factor(R-Free) 0.2349
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9921
    Shell Resolution(Low) 4.0543
    Number of Reflections(R-Free) 284
    Number of Reflections(R-Work) 5125
    R-Factor(R-Work) 0.1867
    R-Factor(R-Free) 0.2376
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0543
    Shell Resolution(Low) 4.1207
    Number of Reflections(R-Free) 305
    Number of Reflections(R-Work) 5094
    R-Factor(R-Work) 0.1703
    R-Factor(R-Free) 0.2219
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1207
    Shell Resolution(Low) 4.1916
    Number of Reflections(R-Free) 256
    Number of Reflections(R-Work) 5174
    R-Factor(R-Work) 0.1647
    R-Factor(R-Free) 0.2303
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1916
    Shell Resolution(Low) 4.2677
    Number of Reflections(R-Free) 242
    Number of Reflections(R-Work) 5178
    R-Factor(R-Work) 0.167
    R-Factor(R-Free) 0.2574
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2677
    Shell Resolution(Low) 4.3497
    Number of Reflections(R-Free) 309
    Number of Reflections(R-Work) 5146
    R-Factor(R-Work) 0.1564
    R-Factor(R-Free) 0.205
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3497
    Shell Resolution(Low) 4.4383
    Number of Reflections(R-Free) 264
    Number of Reflections(R-Work) 5137
    R-Factor(R-Work) 0.1496
    R-Factor(R-Free) 0.1907
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4383
    Shell Resolution(Low) 4.5346
    Number of Reflections(R-Free) 296
    Number of Reflections(R-Work) 5107
    R-Factor(R-Work) 0.1426
    R-Factor(R-Free) 0.1911
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5346
    Shell Resolution(Low) 4.6398
    Number of Reflections(R-Free) 258
    Number of Reflections(R-Work) 5197
    R-Factor(R-Work) 0.1366
    R-Factor(R-Free) 0.1937
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6398
    Shell Resolution(Low) 4.7556
    Number of Reflections(R-Free) 253
    Number of Reflections(R-Work) 5180
    R-Factor(R-Work) 0.1299
    R-Factor(R-Free) 0.1928
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7556
    Shell Resolution(Low) 4.8838
    Number of Reflections(R-Free) 259
    Number of Reflections(R-Work) 5199
    R-Factor(R-Work) 0.1289
    R-Factor(R-Free) 0.2024
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8838
    Shell Resolution(Low) 5.0271
    Number of Reflections(R-Free) 289
    Number of Reflections(R-Work) 5151
    R-Factor(R-Work) 0.1238
    R-Factor(R-Free) 0.1721
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0271
    Shell Resolution(Low) 5.1889
    Number of Reflections(R-Free) 252
    Number of Reflections(R-Work) 5201
    R-Factor(R-Work) 0.1197
    R-Factor(R-Free) 0.1717
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1889
    Shell Resolution(Low) 5.3737
    Number of Reflections(R-Free) 263
    Number of Reflections(R-Work) 5216
    R-Factor(R-Work) 0.1127
    R-Factor(R-Free) 0.1716
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.3737
    Shell Resolution(Low) 5.588
    Number of Reflections(R-Free) 277
    Number of Reflections(R-Work) 5188
    R-Factor(R-Work) 0.1166
    R-Factor(R-Free) 0.1698
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.588
    Shell Resolution(Low) 5.8411
    Number of Reflections(R-Free) 275
    Number of Reflections(R-Work) 5208
    R-Factor(R-Work) 0.1178
    R-Factor(R-Free) 0.1855
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.8411
    Shell Resolution(Low) 6.1475
    Number of Reflections(R-Free) 246
    Number of Reflections(R-Work) 5217
    R-Factor(R-Work) 0.1223
    R-Factor(R-Free) 0.179
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.1475
    Shell Resolution(Low) 6.5303
    Number of Reflections(R-Free) 263
    Number of Reflections(R-Work) 5235
    R-Factor(R-Work) 0.1302
    R-Factor(R-Free) 0.1764
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.5303
    Shell Resolution(Low) 7.0306
    Number of Reflections(R-Free) 277
    Number of Reflections(R-Work) 5242
    R-Factor(R-Work) 0.1341
    R-Factor(R-Free) 0.1898
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.0306
    Shell Resolution(Low) 7.731
    Number of Reflections(R-Free) 281
    Number of Reflections(R-Work) 5240
    R-Factor(R-Work) 0.1315
    R-Factor(R-Free) 0.1936
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.731
    Shell Resolution(Low) 8.8334
    Number of Reflections(R-Free) 273
    Number of Reflections(R-Work) 5296
    R-Factor(R-Work) 0.1323
    R-Factor(R-Free) 0.1768
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.8334
    Shell Resolution(Low) 11.0686
    Number of Reflections(R-Free) 281
    Number of Reflections(R-Work) 5299
    R-Factor(R-Work) 0.1484
    R-Factor(R-Free) 0.1933
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 11.0686
    Shell Resolution(Low) 34.6456
    Number of Reflections(R-Free) 289
    Number of Reflections(R-Work) 5209
    R-Factor(R-Work) 0.2165
    R-Factor(R-Free) 0.2362
    Percent Reflections(Observed) 94.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 19.484
    f_plane_restr 0.009
    f_chiral_restr 0.086
    f_angle_d 1.495
    f_bond_d 0.012
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 19088
    Nucleic Acid Atoms 32507
    Heterogen Atoms 256
    Solvent Atoms 239
     
     
  •   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