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X-RAY DIFFRACTION
Materials and Methods page
4DR7
  •   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 = 402.49 α = 90
    b = 402.49 β = 90
    c = 174.79 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 PIXEL
    Type DECTRIS PILATUS 6M
    Collection Date 2011-06-28
     
    Diffraction Radiation
    Monochromator double crystal Si(111) monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X25
    Wavelength List 1.1
    Site NSLS
    Beamline X25
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) -3.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 3.75
    Resolution(Low) 50
    Number Reflections(All) 146049
    Number Reflections(Observed) 146049
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.136
    B(Isotropic) From Wilson Plot 121.622
     
    High Resolution Shell Details
    Resolution(High) 3.75
    Resolution(Low) 3.85
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.014
    Mean I Over Sigma(Observed) 1.99
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 3.75
    Resolution(Low) 48.909
    Cut-off Sigma(F) 1.99
    Number of Reflections(all) 146005
    Number of Reflections(Observed) 146005
    Number of Reflections(R-Free) 7300
    Percent Reflections(Observed) 99.94
    R-Factor(Observed) 0.1507
    R-Work 0.1481
    R-Free 0.2008
    R-Free Selection Details FROM PDB ENTRY 2VQE
     
    Temperature Factor Modeling
    Mean Isotropic B Value 146.218
    Anisotropic B[1][1] -3.9266
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -3.9266
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 13.4395
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.75
    Shell Resolution(Low) 3.7926
    Number of Reflections(R-Free) 237
    Number of Reflections(R-Work) 4584
    R-Factor(R-Work) 0.2365
    R-Factor(R-Free) 0.2965
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7926
    Shell Resolution(Low) 3.8372
    Number of Reflections(R-Free) 256
    Number of Reflections(R-Work) 4543
    R-Factor(R-Work) 0.235
    R-Factor(R-Free) 0.2926
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8372
    Shell Resolution(Low) 3.8839
    Number of Reflections(R-Free) 281
    Number of Reflections(R-Work) 4552
    R-Factor(R-Work) 0.231
    R-Factor(R-Free) 0.2723
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8839
    Shell Resolution(Low) 3.9331
    Number of Reflections(R-Free) 194
    Number of Reflections(R-Work) 4570
    R-Factor(R-Work) 0.2265
    R-Factor(R-Free) 0.2823
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9331
    Shell Resolution(Low) 3.9848
    Number of Reflections(R-Free) 251
    Number of Reflections(R-Work) 4580
    R-Factor(R-Work) 0.1972
    R-Factor(R-Free) 0.2281
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9848
    Shell Resolution(Low) 4.0394
    Number of Reflections(R-Free) 233
    Number of Reflections(R-Work) 4587
    R-Factor(R-Work) 0.1884
    R-Factor(R-Free) 0.2796
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0394
    Shell Resolution(Low) 4.0971
    Number of Reflections(R-Free) 228
    Number of Reflections(R-Work) 4582
    R-Factor(R-Work) 0.1756
    R-Factor(R-Free) 0.2489
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0971
    Shell Resolution(Low) 4.1582
    Number of Reflections(R-Free) 241
    Number of Reflections(R-Work) 4596
    R-Factor(R-Work) 0.1781
    R-Factor(R-Free) 0.2498
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1582
    Shell Resolution(Low) 4.2231
    Number of Reflections(R-Free) 249
    Number of Reflections(R-Work) 4554
    R-Factor(R-Work) 0.1697
    R-Factor(R-Free) 0.2403
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2231
    Shell Resolution(Low) 4.2923
    Number of Reflections(R-Free) 231
    Number of Reflections(R-Work) 4594
    R-Factor(R-Work) 0.1628
    R-Factor(R-Free) 0.222
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2923
    Shell Resolution(Low) 4.3663
    Number of Reflections(R-Free) 245
    Number of Reflections(R-Work) 4593
    R-Factor(R-Work) 0.149
    R-Factor(R-Free) 0.2084
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3663
    Shell Resolution(Low) 4.4456
    Number of Reflections(R-Free) 256
    Number of Reflections(R-Work) 4544
    R-Factor(R-Work) 0.1412
    R-Factor(R-Free) 0.1973
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4456
    Shell Resolution(Low) 4.5311
    Number of Reflections(R-Free) 209
    Number of Reflections(R-Work) 4637
    R-Factor(R-Work) 0.1323
    R-Factor(R-Free) 0.1999
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5311
    Shell Resolution(Low) 4.6235
    Number of Reflections(R-Free) 230
    Number of Reflections(R-Work) 4620
    R-Factor(R-Work) 0.131
    R-Factor(R-Free) 0.2028
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6235
    Shell Resolution(Low) 4.724
    Number of Reflections(R-Free) 243
    Number of Reflections(R-Work) 4603
    R-Factor(R-Work) 0.1283
    R-Factor(R-Free) 0.2003
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.724
    Shell Resolution(Low) 4.8337
    Number of Reflections(R-Free) 244
    Number of Reflections(R-Work) 4578
    R-Factor(R-Work) 0.1211
    R-Factor(R-Free) 0.1743
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8337
    Shell Resolution(Low) 4.9545
    Number of Reflections(R-Free) 211
    Number of Reflections(R-Work) 4633
    R-Factor(R-Work) 0.1155
    R-Factor(R-Free) 0.1891
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9545
    Shell Resolution(Low) 5.0883
    Number of Reflections(R-Free) 238
    Number of Reflections(R-Work) 4621
    R-Factor(R-Work) 0.1151
    R-Factor(R-Free) 0.1774
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0883
    Shell Resolution(Low) 5.2379
    Number of Reflections(R-Free) 242
    Number of Reflections(R-Work) 4607
    R-Factor(R-Work) 0.1183
    R-Factor(R-Free) 0.168
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2379
    Shell Resolution(Low) 5.4068
    Number of Reflections(R-Free) 265
    Number of Reflections(R-Work) 4583
    R-Factor(R-Work) 0.1198
    R-Factor(R-Free) 0.182
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.4068
    Shell Resolution(Low) 5.5997
    Number of Reflections(R-Free) 229
    Number of Reflections(R-Work) 4647
    R-Factor(R-Work) 0.1162
    R-Factor(R-Free) 0.1788
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.5997
    Shell Resolution(Low) 5.8236
    Number of Reflections(R-Free) 247
    Number of Reflections(R-Work) 4628
    R-Factor(R-Work) 0.1091
    R-Factor(R-Free) 0.1663
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.8236
    Shell Resolution(Low) 6.0882
    Number of Reflections(R-Free) 264
    Number of Reflections(R-Work) 4614
    R-Factor(R-Work) 0.1164
    R-Factor(R-Free) 0.1742
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.0882
    Shell Resolution(Low) 6.4085
    Number of Reflections(R-Free) 239
    Number of Reflections(R-Work) 4650
    R-Factor(R-Work) 0.1192
    R-Factor(R-Free) 0.1876
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.4085
    Shell Resolution(Low) 6.809
    Number of Reflections(R-Free) 232
    Number of Reflections(R-Work) 4674
    R-Factor(R-Work) 0.1163
    R-Factor(R-Free) 0.1759
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.809
    Shell Resolution(Low) 7.3332
    Number of Reflections(R-Free) 243
    Number of Reflections(R-Work) 4685
    R-Factor(R-Work) 0.1081
    R-Factor(R-Free) 0.1622
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.3332
    Shell Resolution(Low) 8.0682
    Number of Reflections(R-Free) 249
    Number of Reflections(R-Work) 4682
    R-Factor(R-Work) 0.1157
    R-Factor(R-Free) 0.1733
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.0682
    Shell Resolution(Low) 9.2288
    Number of Reflections(R-Free) 275
    Number of Reflections(R-Work) 4690
    R-Factor(R-Work) 0.1268
    R-Factor(R-Free) 0.1779
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 9.2288
    Shell Resolution(Low) 11.6017
    Number of Reflections(R-Free) 264
    Number of Reflections(R-Work) 4751
    R-Factor(R-Work) 0.1394
    R-Factor(R-Free) 0.1842
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 11.6017
    Shell Resolution(Low) 48.9133
    Number of Reflections(R-Free) 274
    Number of Reflections(R-Work) 4923
    R-Factor(R-Work) 0.2187
    R-Factor(R-Free) 0.232
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 20.411
    f_plane_restr 0.009
    f_chiral_restr 0.086
    f_angle_d 1.627
    f_bond_d 0.014
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 19127
    Nucleic Acid Atoms 33073
    Heterogen Atoms 386
    Solvent Atoms 892
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) xds
    Data Reduction (data scaling) XSCALE
    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 Xscale