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X-RAY DIFFRACTION
Materials and Methods page
4JI2
  •   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 = 402.45 α = 90
    b = 402.45 β = 90
    c = 174.41 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 2011-08-03
     
    Diffraction Radiation
    Monochromator Kohzu HLD8-24 Monochromator
    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) 3.64
    Resolution(Low) 50
    Number Reflections(All) 157605
    Number Reflections(Observed) 157605
    Percent Possible(Observed) 98.9
    R Merge I(Observed) 0.102
    B(Isotropic) From Wilson Plot 111.09
     
    High Resolution Shell Details
    Resolution(High) 3.64
    Resolution(Low) 3.86
    Percent Possible(All) 95.2
    R Merge I(Observed) 0.709
    Mean I Over Sigma(Observed) 1.84
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 3.64
    Resolution(Low) 48.335
    Cut-off Sigma(F) 1.99
    Number of Reflections(all) 157539
    Number of Reflections(Observed) 157539
    Number of Reflections(R-Free) 7889
    Percent Reflections(Observed) 98.89
    R-Factor(Observed) 0.1582
    R-Work 0.1554
    R-Free 0.2113
    R-Free Selection Details FROM PDB ENTRY 2VQE
     
    Temperature Factor Modeling
    Mean Isotropic B Value 153.943
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6389
    Shell Resolution(Low) 3.6802
    Number of Reflections(R-Free) 212
    Number of Reflections(R-Work) 3813
    R-Factor(R-Work) 0.2835
    R-Factor(R-Free) 0.3354
    Percent Reflections(Observed) 77.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6802
    Shell Resolution(Low) 3.7235
    Number of Reflections(R-Free) 252
    Number of Reflections(R-Work) 5014
    R-Factor(R-Work) 0.2676
    R-Factor(R-Free) 0.3259
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7235
    Shell Resolution(Low) 3.7689
    Number of Reflections(R-Free) 266
    Number of Reflections(R-Work) 4964
    R-Factor(R-Work) 0.2399
    R-Factor(R-Free) 0.2996
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7689
    Shell Resolution(Low) 3.8166
    Number of Reflections(R-Free) 282
    Number of Reflections(R-Work) 4980
    R-Factor(R-Work) 0.2282
    R-Factor(R-Free) 0.2857
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8166
    Shell Resolution(Low) 3.8668
    Number of Reflections(R-Free) 284
    Number of Reflections(R-Work) 4961
    R-Factor(R-Work) 0.2183
    R-Factor(R-Free) 0.2896
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8668
    Shell Resolution(Low) 3.9197
    Number of Reflections(R-Free) 236
    Number of Reflections(R-Work) 5005
    R-Factor(R-Work) 0.2134
    R-Factor(R-Free) 0.2479
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9197
    Shell Resolution(Low) 3.9757
    Number of Reflections(R-Free) 261
    Number of Reflections(R-Work) 5023
    R-Factor(R-Work) 0.2077
    R-Factor(R-Free) 0.2582
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9757
    Shell Resolution(Low) 4.035
    Number of Reflections(R-Free) 261
    Number of Reflections(R-Work) 4975
    R-Factor(R-Work) 0.1991
    R-Factor(R-Free) 0.2586
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.035
    Shell Resolution(Low) 4.0981
    Number of Reflections(R-Free) 253
    Number of Reflections(R-Work) 5009
    R-Factor(R-Work) 0.1879
    R-Factor(R-Free) 0.2733
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0981
    Shell Resolution(Low) 4.1652
    Number of Reflections(R-Free) 264
    Number of Reflections(R-Work) 4992
    R-Factor(R-Work) 0.1786
    R-Factor(R-Free) 0.2574
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1652
    Shell Resolution(Low) 4.237
    Number of Reflections(R-Free) 264
    Number of Reflections(R-Work) 4991
    R-Factor(R-Work) 0.169
    R-Factor(R-Free) 0.2274
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.237
    Shell Resolution(Low) 4.314
    Number of Reflections(R-Free) 260
    Number of Reflections(R-Work) 4991
    R-Factor(R-Work) 0.1639
    R-Factor(R-Free) 0.2263
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.314
    Shell Resolution(Low) 4.3969
    Number of Reflections(R-Free) 259
    Number of Reflections(R-Work) 5018
    R-Factor(R-Work) 0.1535
    R-Factor(R-Free) 0.2261
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3969
    Shell Resolution(Low) 4.4866
    Number of Reflections(R-Free) 267
    Number of Reflections(R-Work) 5025
    R-Factor(R-Work) 0.1401
    R-Factor(R-Free) 0.1881
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4866
    Shell Resolution(Low) 4.5841
    Number of Reflections(R-Free) 237
    Number of Reflections(R-Work) 5033
    R-Factor(R-Work) 0.1362
    R-Factor(R-Free) 0.2017
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5841
    Shell Resolution(Low) 4.6906
    Number of Reflections(R-Free) 262
    Number of Reflections(R-Work) 5024
    R-Factor(R-Work) 0.1385
    R-Factor(R-Free) 0.2157
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6906
    Shell Resolution(Low) 4.8078
    Number of Reflections(R-Free) 258
    Number of Reflections(R-Work) 5008
    R-Factor(R-Work) 0.1301
    R-Factor(R-Free) 0.2008
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8078
    Shell Resolution(Low) 4.9377
    Number of Reflections(R-Free) 244
    Number of Reflections(R-Work) 5032
    R-Factor(R-Work) 0.1286
    R-Factor(R-Free) 0.188
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9377
    Shell Resolution(Low) 5.0828
    Number of Reflections(R-Free) 257
    Number of Reflections(R-Work) 5047
    R-Factor(R-Work) 0.1228
    R-Factor(R-Free) 0.1936
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0828
    Shell Resolution(Low) 5.2467
    Number of Reflections(R-Free) 274
    Number of Reflections(R-Work) 5008
    R-Factor(R-Work) 0.1245
    R-Factor(R-Free) 0.1662
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2467
    Shell Resolution(Low) 5.434
    Number of Reflections(R-Free) 291
    Number of Reflections(R-Work) 5022
    R-Factor(R-Work) 0.122
    R-Factor(R-Free) 0.2008
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.434
    Shell Resolution(Low) 5.6512
    Number of Reflections(R-Free) 235
    Number of Reflections(R-Work) 5062
    R-Factor(R-Work) 0.121
    R-Factor(R-Free) 0.1769
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.6512
    Shell Resolution(Low) 5.908
    Number of Reflections(R-Free) 274
    Number of Reflections(R-Work) 5044
    R-Factor(R-Work) 0.1251
    R-Factor(R-Free) 0.1939
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.908
    Shell Resolution(Low) 6.2189
    Number of Reflections(R-Free) 296
    Number of Reflections(R-Work) 5031
    R-Factor(R-Work) 0.1238
    R-Factor(R-Free) 0.1988
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.2189
    Shell Resolution(Low) 6.6076
    Number of Reflections(R-Free) 253
    Number of Reflections(R-Work) 5079
    R-Factor(R-Work) 0.1219
    R-Factor(R-Free) 0.1899
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.6076
    Shell Resolution(Low) 7.1163
    Number of Reflections(R-Free) 245
    Number of Reflections(R-Work) 5088
    R-Factor(R-Work) 0.1226
    R-Factor(R-Free) 0.1681
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.1163
    Shell Resolution(Low) 7.8298
    Number of Reflections(R-Free) 264
    Number of Reflections(R-Work) 5124
    R-Factor(R-Work) 0.1294
    R-Factor(R-Free) 0.1867
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.8298
    Shell Resolution(Low) 8.9565
    Number of Reflections(R-Free) 299
    Number of Reflections(R-Work) 5044
    R-Factor(R-Work) 0.1423
    R-Factor(R-Free) 0.193
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.9565
    Shell Resolution(Low) 11.2607
    Number of Reflections(R-Free) 296
    Number of Reflections(R-Work) 5102
    R-Factor(R-Work) 0.1424
    R-Factor(R-Free) 0.2039
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 11.2607
    Shell Resolution(Low) 48.3397
    Number of Reflections(R-Free) 283
    Number of Reflections(R-Work) 5141
    R-Factor(R-Work) 0.1908
    R-Factor(R-Free) 0.203
    Percent Reflections(Observed) 95.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 20.382
    f_plane_restr 0.008
    f_chiral_restr 0.093
    f_angle_d 1.915
    f_bond_d 0.013
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 19093
    Nucleic Acid Atoms 32507
    Heterogen Atoms 295
    Solvent Atoms 275
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    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