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X-RAY DIFFRACTION
Materials and Methods page
4F4K
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5.8
    Temperature 290.0
    Details 53% Saturated Ammonium Sulfate, 2.5% MPD, 10mM MnSO4, 100mM MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 93.81 α = 90
    b = 109.22 β = 90
    c = 150.58 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 225 mm CCD
    Collection Date 2011-11-19
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 22-BM
    Wavelength List 1.0000
    Site APS
    Beamline 22-BM
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.6
    Resolution(Low) 50
    Number Reflections(Observed) 187320
    Percent Possible(Observed) 92.1
    R Merge I(Observed) 0.045
    B(Isotropic) From Wilson Plot 27.797
    Redundancy 5.7
     
    High Resolution Shell Details
    Resolution(High) 1.6
    Resolution(Low) 1.69
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.504
    Mean I Over Sigma(Observed) 3.61
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 1.6
    Resolution(Low) 30.062
    Cut-off Sigma(F) 2.35
    Number of Reflections(Observed) 179455
    Number of Reflections(R-Free) 8168
    Percent Reflections(Observed) 88.24
    R-Factor(Observed) 0.1719
    R-Work 0.1709
    R-Free 0.1941
    R-Free Selection Details Inherited free reflections from 2HVI plus 5% randomly generated reflections beyond 1.98 resolution
     
    Temperature Factor Modeling
    Data Not Available
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6
    Shell Resolution(Low) 1.6182
    Number of Reflections(R-Free) 289
    Number of Reflections(R-Work) 5483
    R-Factor(R-Work) 0.2346
    R-Factor(R-Free) 0.2676
    Percent Reflections(Observed) 86.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6182
    Shell Resolution(Low) 1.6372
    Number of Reflections(R-Free) 294
    Number of Reflections(R-Work) 5582
    R-Factor(R-Work) 0.225
    R-Factor(R-Free) 0.26
    Percent Reflections(Observed) 88.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6372
    Shell Resolution(Low) 1.6572
    Number of Reflections(R-Free) 300
    Number of Reflections(R-Work) 5697
    R-Factor(R-Work) 0.2139
    R-Factor(R-Free) 0.2446
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6572
    Shell Resolution(Low) 1.6782
    Number of Reflections(R-Free) 304
    Number of Reflections(R-Work) 5788
    R-Factor(R-Work) 0.2119
    R-Factor(R-Free) 0.2553
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6782
    Shell Resolution(Low) 1.7002
    Number of Reflections(R-Free) 303
    Number of Reflections(R-Work) 5748
    R-Factor(R-Work) 0.2007
    R-Factor(R-Free) 0.2346
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7002
    Shell Resolution(Low) 1.7235
    Number of Reflections(R-Free) 312
    Number of Reflections(R-Work) 5938
    R-Factor(R-Work) 0.1942
    R-Factor(R-Free) 0.2383
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7235
    Shell Resolution(Low) 1.7481
    Number of Reflections(R-Free) 313
    Number of Reflections(R-Work) 5938
    R-Factor(R-Work) 0.1887
    R-Factor(R-Free) 0.231
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7481
    Shell Resolution(Low) 1.7742
    Number of Reflections(R-Free) 315
    Number of Reflections(R-Work) 5986
    R-Factor(R-Work) 0.1874
    R-Factor(R-Free) 0.2314
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7742
    Shell Resolution(Low) 1.802
    Number of Reflections(R-Free) 317
    Number of Reflections(R-Work) 6017
    R-Factor(R-Work) 0.1801
    R-Factor(R-Free) 0.2141
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.802
    Shell Resolution(Low) 1.8315
    Number of Reflections(R-Free) 317
    Number of Reflections(R-Work) 6035
    R-Factor(R-Work) 0.1791
    R-Factor(R-Free) 0.2178
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8315
    Shell Resolution(Low) 1.8631
    Number of Reflections(R-Free) 320
    Number of Reflections(R-Work) 6070
    R-Factor(R-Work) 0.1757
    R-Factor(R-Free) 0.2077
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8631
    Shell Resolution(Low) 1.8969
    Number of Reflections(R-Free) 258
    Number of Reflections(R-Work) 4910
    R-Factor(R-Work) 0.1758
    R-Factor(R-Free) 0.2097
    Percent Reflections(Observed) 87.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9334
    Shell Resolution(Low) 1.9729
    Number of Reflections(R-Free) 221
    Number of Reflections(R-Work) 4196
    R-Factor(R-Work) 0.1762
    R-Factor(R-Free) 0.2379
    Percent Reflections(Observed) 86.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9729
    Shell Resolution(Low) 2.0158
    Number of Reflections(R-Free) 232
    Number of Reflections(R-Work) 6297
    R-Factor(R-Work) 0.1708
    R-Factor(R-Free) 0.1878
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0158
    Shell Resolution(Low) 2.0627
    Number of Reflections(R-Free) 226
    Number of Reflections(R-Work) 6434
    R-Factor(R-Work) 0.1621
    R-Factor(R-Free) 0.1822
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0627
    Shell Resolution(Low) 2.1142
    Number of Reflections(R-Free) 245
    Number of Reflections(R-Work) 6398
    R-Factor(R-Work) 0.1579
    R-Factor(R-Free) 0.1695
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1142
    Shell Resolution(Low) 2.1714
    Number of Reflections(R-Free) 258
    Number of Reflections(R-Work) 6390
    R-Factor(R-Work) 0.1586
    R-Factor(R-Free) 0.1812
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1714
    Shell Resolution(Low) 2.2352
    Number of Reflections(R-Free) 244
    Number of Reflections(R-Work) 5096
    R-Factor(R-Work) 0.1592
    R-Factor(R-Free) 0.169
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2352
    Shell Resolution(Low) 2.3074
    Number of Reflections(R-Free) 84
    Number of Reflections(R-Work) 2510
    R-Factor(R-Work) 0.1581
    R-Factor(R-Free) 0.1864
    Percent Reflections(Observed) 88.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3074
    Shell Resolution(Low) 2.3898
    Number of Reflections(R-Free) 263
    Number of Reflections(R-Work) 6457
    R-Factor(R-Work) 0.1589
    R-Factor(R-Free) 0.1826
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3898
    Shell Resolution(Low) 2.4854
    Number of Reflections(R-Free) 258
    Number of Reflections(R-Work) 6468
    R-Factor(R-Work) 0.1629
    R-Factor(R-Free) 0.1935
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4854
    Shell Resolution(Low) 2.5985
    Number of Reflections(R-Free) 269
    Number of Reflections(R-Work) 6453
    R-Factor(R-Work) 0.1646
    R-Factor(R-Free) 0.2005
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5985
    Shell Resolution(Low) 2.7354
    Number of Reflections(R-Free) 279
    Number of Reflections(R-Work) 6481
    R-Factor(R-Work) 0.172
    R-Factor(R-Free) 0.2034
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7354
    Shell Resolution(Low) 2.9067
    Number of Reflections(R-Free) 292
    Number of Reflections(R-Work) 6471
    R-Factor(R-Work) 0.1769
    R-Factor(R-Free) 0.2081
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9067
    Shell Resolution(Low) 3.1309
    Number of Reflections(R-Free) 311
    Number of Reflections(R-Work) 6491
    R-Factor(R-Work) 0.1787
    R-Factor(R-Free) 0.1908
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1309
    Shell Resolution(Low) 3.4455
    Number of Reflections(R-Free) 337
    Number of Reflections(R-Work) 6456
    R-Factor(R-Work) 0.1657
    R-Factor(R-Free) 0.1788
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4455
    Shell Resolution(Low) 3.9432
    Number of Reflections(R-Free) 326
    Number of Reflections(R-Work) 6386
    R-Factor(R-Work) 0.1565
    R-Factor(R-Free) 0.1748
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9432
    Shell Resolution(Low) 4.9643
    Number of Reflections(R-Free) 339
    Number of Reflections(R-Work) 6515
    R-Factor(R-Work) 0.1456
    R-Factor(R-Free) 0.1699
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9643
    Shell Resolution(Low) 30.0675
    Number of Reflections(R-Free) 342
    Number of Reflections(R-Work) 6596
    R-Factor(R-Work) 0.1971
    R-Factor(R-Free) 0.1995
    Percent Reflections(Observed) 97.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 15.39
    f_plane_restr 0.007
    f_chiral_restr 0.076
    f_angle_d 1.353
    f_bond_d 0.011
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 9294
    Nucleic Acid Atoms 828
    Heterogen Atoms 54
    Solvent Atoms 1436
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Refinement PHENIX (phenix.refine: dev_1026)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction Xscale