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X-RAY DIFFRACTION
Materials and Methods page
4JI5
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.5
    Temperature 277.0
    Details MPD , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 399.62 α = 90
    b = 399.62 β = 90
    c = 216.07 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 2012-03-01
     
    Diffraction Radiation
    Monochromator Monochromator: Double silicon(111) crystal 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 0.98
    Site NSLS
    Beamline X25
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) -3.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 3.85
    Resolution(Low) 50
    Number Reflections(All) 163037
    Number Reflections(Observed) 163037
    Percent Possible(Observed) 99.3
    R Merge I(Observed) 0.117
    B(Isotropic) From Wilson Plot 144.028
     
    High Resolution Shell Details
    Resolution(High) 3.85
    Resolution(Low) 3.95
    Percent Possible(All) 99.9
    R Merge I(Observed) 0.011
    Mean I Over Sigma(Observed) 1.9
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 3.85
    Resolution(Low) 47.286
    Cut-off Sigma(F) 1.99
    Number of Reflections(all) 162952
    Number of Reflections(Observed) 162952
    Number of Reflections(R-Free) 8210
    Percent Reflections(Observed) 99.27
    R-Factor(Observed) 0.1553
    R-Work 0.1528
    R-Free 0.202
    R-Free Selection Details FROM PDB ENTRY 2VQE
     
    Temperature Factor Modeling
    Mean Isotropic B Value 162.958
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.85
    Shell Resolution(Low) 3.8937
    Number of Reflections(R-Free) 304
    Number of Reflections(R-Work) 5050
    R-Factor(R-Work) 0.2588
    R-Factor(R-Free) 0.3377
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8937
    Shell Resolution(Low) 3.9395
    Number of Reflections(R-Free) 283
    Number of Reflections(R-Work) 5137
    R-Factor(R-Work) 0.232
    R-Factor(R-Free) 0.2945
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9395
    Shell Resolution(Low) 3.9875
    Number of Reflections(R-Free) 278
    Number of Reflections(R-Work) 5147
    R-Factor(R-Work) 0.232
    R-Factor(R-Free) 0.2858
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9875
    Shell Resolution(Low) 4.038
    Number of Reflections(R-Free) 275
    Number of Reflections(R-Work) 5124
    R-Factor(R-Work) 0.2159
    R-Factor(R-Free) 0.2814
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.038
    Shell Resolution(Low) 4.0911
    Number of Reflections(R-Free) 263
    Number of Reflections(R-Work) 5142
    R-Factor(R-Work) 0.2065
    R-Factor(R-Free) 0.2765
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0911
    Shell Resolution(Low) 4.1471
    Number of Reflections(R-Free) 288
    Number of Reflections(R-Work) 5116
    R-Factor(R-Work) 0.2011
    R-Factor(R-Free) 0.2486
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1471
    Shell Resolution(Low) 4.2063
    Number of Reflections(R-Free) 279
    Number of Reflections(R-Work) 5156
    R-Factor(R-Work) 0.1819
    R-Factor(R-Free) 0.2271
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2063
    Shell Resolution(Low) 4.269
    Number of Reflections(R-Free) 240
    Number of Reflections(R-Work) 5146
    R-Factor(R-Work) 0.1751
    R-Factor(R-Free) 0.2289
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.269
    Shell Resolution(Low) 4.3357
    Number of Reflections(R-Free) 270
    Number of Reflections(R-Work) 5166
    R-Factor(R-Work) 0.1671
    R-Factor(R-Free) 0.2234
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3357
    Shell Resolution(Low) 4.4067
    Number of Reflections(R-Free) 282
    Number of Reflections(R-Work) 5115
    R-Factor(R-Work) 0.1631
    R-Factor(R-Free) 0.2079
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4067
    Shell Resolution(Low) 4.4827
    Number of Reflections(R-Free) 257
    Number of Reflections(R-Work) 5163
    R-Factor(R-Work) 0.1634
    R-Factor(R-Free) 0.2205
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4827
    Shell Resolution(Low) 4.5641
    Number of Reflections(R-Free) 229
    Number of Reflections(R-Work) 5171
    R-Factor(R-Work) 0.1568
    R-Factor(R-Free) 0.2202
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5641
    Shell Resolution(Low) 4.6518
    Number of Reflections(R-Free) 271
    Number of Reflections(R-Work) 5143
    R-Factor(R-Work) 0.1508
    R-Factor(R-Free) 0.2095
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6518
    Shell Resolution(Low) 4.7467
    Number of Reflections(R-Free) 291
    Number of Reflections(R-Work) 5126
    R-Factor(R-Work) 0.1429
    R-Factor(R-Free) 0.1988
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7467
    Shell Resolution(Low) 4.8498
    Number of Reflections(R-Free) 260
    Number of Reflections(R-Work) 5133
    R-Factor(R-Work) 0.1321
    R-Factor(R-Free) 0.1938
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8498
    Shell Resolution(Low) 4.9625
    Number of Reflections(R-Free) 252
    Number of Reflections(R-Work) 5186
    R-Factor(R-Work) 0.1386
    R-Factor(R-Free) 0.196
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9625
    Shell Resolution(Low) 5.0865
    Number of Reflections(R-Free) 266
    Number of Reflections(R-Work) 5180
    R-Factor(R-Work) 0.1314
    R-Factor(R-Free) 0.1809
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0865
    Shell Resolution(Low) 5.2238
    Number of Reflections(R-Free) 285
    Number of Reflections(R-Work) 5149
    R-Factor(R-Work) 0.1239
    R-Factor(R-Free) 0.1809
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2238
    Shell Resolution(Low) 5.3773
    Number of Reflections(R-Free) 275
    Number of Reflections(R-Work) 5146
    R-Factor(R-Work) 0.1215
    R-Factor(R-Free) 0.1662
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.3773
    Shell Resolution(Low) 5.5506
    Number of Reflections(R-Free) 282
    Number of Reflections(R-Work) 5165
    R-Factor(R-Work) 0.1171
    R-Factor(R-Free) 0.1767
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.5506
    Shell Resolution(Low) 5.7487
    Number of Reflections(R-Free) 250
    Number of Reflections(R-Work) 5151
    R-Factor(R-Work) 0.1163
    R-Factor(R-Free) 0.1685
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.7487
    Shell Resolution(Low) 5.9784
    Number of Reflections(R-Free) 254
    Number of Reflections(R-Work) 5196
    R-Factor(R-Work) 0.1162
    R-Factor(R-Free) 0.1738
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.9784
    Shell Resolution(Low) 6.2499
    Number of Reflections(R-Free) 286
    Number of Reflections(R-Work) 5125
    R-Factor(R-Work) 0.1173
    R-Factor(R-Free) 0.1728
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.2499
    Shell Resolution(Low) 6.5786
    Number of Reflections(R-Free) 287
    Number of Reflections(R-Work) 5166
    R-Factor(R-Work) 0.1206
    R-Factor(R-Free) 0.1789
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.5786
    Shell Resolution(Low) 6.9896
    Number of Reflections(R-Free) 269
    Number of Reflections(R-Work) 5190
    R-Factor(R-Work) 0.1172
    R-Factor(R-Free) 0.1676
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.9896
    Shell Resolution(Low) 7.5273
    Number of Reflections(R-Free) 275
    Number of Reflections(R-Work) 5162
    R-Factor(R-Work) 0.1195
    R-Factor(R-Free) 0.1615
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.5273
    Shell Resolution(Low) 8.2811
    Number of Reflections(R-Free) 287
    Number of Reflections(R-Work) 5197
    R-Factor(R-Work) 0.1268
    R-Factor(R-Free) 0.1799
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.2811
    Shell Resolution(Low) 9.4711
    Number of Reflections(R-Free) 279
    Number of Reflections(R-Work) 5192
    R-Factor(R-Work) 0.1479
    R-Factor(R-Free) 0.1965
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 9.4711
    Shell Resolution(Low) 11.901
    Number of Reflections(R-Free) 296
    Number of Reflections(R-Work) 5190
    R-Factor(R-Work) 0.1475
    R-Factor(R-Free) 0.1903
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 11.901
    Shell Resolution(Low) 47.2898
    Number of Reflections(R-Free) 297
    Number of Reflections(R-Work) 5312
    R-Factor(R-Work) 0.214
    R-Factor(R-Free) 0.2385
    Percent Reflections(Observed) 96.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 19.943
    f_plane_restr 0.009
    f_chiral_restr 0.094
    f_angle_d 1.973
    f_bond_d 0.013
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 19088
    Nucleic Acid Atoms 32550
    Heterogen Atoms 174
    Solvent Atoms 279
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CBASS
    Data Reduction (intensity integration) XSCALE
    Data Reduction (data scaling) XSCALE
    Structure Solution PHENIX (phenix.refine: dev_1119)
    Structure Refinement PHENIX (phenix.refine: dev_1119)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction Xscale