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X-RAY DIFFRACTION
Materials and Methods page
4F2R
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5.8
    Temperature 290.0
    Details 47%-49% Saturated Ammonium Sulfate, 2.5% MPD, 10mM MgSO4, 100mM MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 93.22 α = 90
    b = 108.48 β = 90
    c = 150.95 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 225 mm CCD
    Collection Date 2011-10-30
     
    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) 1.63
    Resolution(Low) 50
    Number Reflections(Observed) 190429
    Percent Possible(Observed) 100.0
    R Merge I(Observed) 0.063
    B(Isotropic) From Wilson Plot 29.124
    Redundancy 10.0
     
    High Resolution Shell Details
    Resolution(High) 1.63
    Resolution(Low) 1.73
    Percent Possible(All) 99.8
    R Merge I(Observed) 0.506
    Mean I Over Sigma(Observed) 3.38
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 1.63
    Resolution(Low) 34.98
    Cut-off Sigma(F) 2.35
    Number of Reflections(Observed) 184317
    Number of Reflections(R-Free) 8311
    Percent Reflections(Observed) 96.77
    R-Factor(Observed) 0.1708
    R-Work 0.1698
    R-Free 0.1924
    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) 1.63
    Shell Resolution(Low) 1.6485
    Number of Reflections(R-Free) 267
    Number of Reflections(R-Work) 5062
    R-Factor(R-Work) 0.2473
    R-Factor(R-Free) 0.266
    Percent Reflections(Observed) 85.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6485
    Shell Resolution(Low) 1.6679
    Number of Reflections(R-Free) 278
    Number of Reflections(R-Work) 5282
    R-Factor(R-Work) 0.2354
    R-Factor(R-Free) 0.2498
    Percent Reflections(Observed) 88.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6679
    Shell Resolution(Low) 1.6883
    Number of Reflections(R-Free) 281
    Number of Reflections(R-Work) 5334
    R-Factor(R-Work) 0.2233
    R-Factor(R-Free) 0.2535
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6883
    Shell Resolution(Low) 1.7096
    Number of Reflections(R-Free) 285
    Number of Reflections(R-Work) 5421
    R-Factor(R-Work) 0.2183
    R-Factor(R-Free) 0.2497
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7096
    Shell Resolution(Low) 1.7321
    Number of Reflections(R-Free) 287
    Number of Reflections(R-Work) 5464
    R-Factor(R-Work) 0.2039
    R-Factor(R-Free) 0.2441
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7321
    Shell Resolution(Low) 1.7559
    Number of Reflections(R-Free) 296
    Number of Reflections(R-Work) 5619
    R-Factor(R-Work) 0.2013
    R-Factor(R-Free) 0.2299
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7559
    Shell Resolution(Low) 1.7809
    Number of Reflections(R-Free) 295
    Number of Reflections(R-Work) 5609
    R-Factor(R-Work) 0.1936
    R-Factor(R-Free) 0.2378
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7809
    Shell Resolution(Low) 1.8075
    Number of Reflections(R-Free) 302
    Number of Reflections(R-Work) 5723
    R-Factor(R-Work) 0.1865
    R-Factor(R-Free) 0.2085
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8075
    Shell Resolution(Low) 1.8358
    Number of Reflections(R-Free) 300
    Number of Reflections(R-Work) 5711
    R-Factor(R-Work) 0.1862
    R-Factor(R-Free) 0.2202
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8358
    Shell Resolution(Low) 1.8659
    Number of Reflections(R-Free) 301
    Number of Reflections(R-Work) 5724
    R-Factor(R-Work) 0.1866
    R-Factor(R-Free) 0.2314
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8659
    Shell Resolution(Low) 1.898
    Number of Reflections(R-Free) 303
    Number of Reflections(R-Work) 5750
    R-Factor(R-Work) 0.1835
    R-Factor(R-Free) 0.2173
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.898
    Shell Resolution(Low) 1.9325
    Number of Reflections(R-Free) 309
    Number of Reflections(R-Work) 5861
    R-Factor(R-Work) 0.1777
    R-Factor(R-Free) 0.2058
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9325
    Shell Resolution(Low) 1.9697
    Number of Reflections(R-Free) 307
    Number of Reflections(R-Work) 5839
    R-Factor(R-Work) 0.1786
    R-Factor(R-Free) 0.2199
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9697
    Shell Resolution(Low) 2.0099
    Number of Reflections(R-Free) 182
    Number of Reflections(R-Work) 6025
    R-Factor(R-Work) 0.1745
    R-Factor(R-Free) 0.2114
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0099
    Shell Resolution(Low) 2.0536
    Number of Reflections(R-Free) 212
    Number of Reflections(R-Work) 6037
    R-Factor(R-Work) 0.1667
    R-Factor(R-Free) 0.1802
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0536
    Shell Resolution(Low) 2.1014
    Number of Reflections(R-Free) 231
    Number of Reflections(R-Work) 6035
    R-Factor(R-Work) 0.1657
    R-Factor(R-Free) 0.1995
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1014
    Shell Resolution(Low) 2.1539
    Number of Reflections(R-Free) 247
    Number of Reflections(R-Work) 6018
    R-Factor(R-Work) 0.1609
    R-Factor(R-Free) 0.178
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1539
    Shell Resolution(Low) 2.2121
    Number of Reflections(R-Free) 264
    Number of Reflections(R-Work) 6056
    R-Factor(R-Work) 0.1598
    R-Factor(R-Free) 0.1908
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2121
    Shell Resolution(Low) 2.2772
    Number of Reflections(R-Free) 238
    Number of Reflections(R-Work) 6041
    R-Factor(R-Work) 0.1599
    R-Factor(R-Free) 0.1895
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2772
    Shell Resolution(Low) 2.3507
    Number of Reflections(R-Free) 227
    Number of Reflections(R-Work) 6074
    R-Factor(R-Work) 0.1538
    R-Factor(R-Free) 0.1947
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3507
    Shell Resolution(Low) 2.4347
    Number of Reflections(R-Free) 250
    Number of Reflections(R-Work) 6061
    R-Factor(R-Work) 0.1607
    R-Factor(R-Free) 0.1851
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4347
    Shell Resolution(Low) 2.5322
    Number of Reflections(R-Free) 253
    Number of Reflections(R-Work) 6089
    R-Factor(R-Work) 0.1618
    R-Factor(R-Free) 0.1882
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5322
    Shell Resolution(Low) 2.6474
    Number of Reflections(R-Free) 254
    Number of Reflections(R-Work) 6100
    R-Factor(R-Work) 0.1698
    R-Factor(R-Free) 0.1766
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6474
    Shell Resolution(Low) 2.7869
    Number of Reflections(R-Free) 271
    Number of Reflections(R-Work) 6075
    R-Factor(R-Work) 0.1749
    R-Factor(R-Free) 0.2031
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7869
    Shell Resolution(Low) 2.9614
    Number of Reflections(R-Free) 284
    Number of Reflections(R-Work) 6090
    R-Factor(R-Work) 0.1857
    R-Factor(R-Free) 0.2282
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9614
    Shell Resolution(Low) 3.1899
    Number of Reflections(R-Free) 304
    Number of Reflections(R-Work) 6096
    R-Factor(R-Work) 0.1797
    R-Factor(R-Free) 0.1971
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1899
    Shell Resolution(Low) 3.5107
    Number of Reflections(R-Free) 318
    Number of Reflections(R-Work) 6085
    R-Factor(R-Work) 0.1591
    R-Factor(R-Free) 0.1716
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5107
    Shell Resolution(Low) 4.018
    Number of Reflections(R-Free) 314
    Number of Reflections(R-Work) 6139
    R-Factor(R-Work) 0.1487
    R-Factor(R-Free) 0.1536
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.018
    Shell Resolution(Low) 5.0599
    Number of Reflections(R-Free) 321
    Number of Reflections(R-Work) 6197
    R-Factor(R-Work) 0.1413
    R-Factor(R-Free) 0.1634
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0599
    Shell Resolution(Low) 34.988
    Number of Reflections(R-Free) 330
    Number of Reflections(R-Work) 6389
    R-Factor(R-Work) 0.1864
    R-Factor(R-Free) 0.1996
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 15.169
    f_plane_restr 0.007
    f_chiral_restr 0.083
    f_angle_d 1.375
    f_bond_d 0.011
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 9310
    Nucleic Acid Atoms 832
    Heterogen Atoms 120
    Solvent Atoms 1238
     
     
  •   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