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X-RAY DIFFRACTION
Materials and Methods page
4F2S
  •   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 MnSO4, 100mM MES , pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 93.18 α = 90
    b = 108.59 β = 90
    c = 150.99 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) 1.65
    Resolution(Low) 50
    Number Reflections(Observed) 180667
    Percent Possible(Observed) 98.2
    R Merge I(Observed) 0.109
    B(Isotropic) From Wilson Plot 29.445
    Redundancy 10.0
     
    High Resolution Shell Details
    Resolution(High) 1.65
    Resolution(Low) 1.75
    Percent Possible(All) 89.1
    R Merge I(Observed) 0.509
    Mean I Over Sigma(Observed) 3.72
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 1.651
    Resolution(Low) 34.19
    Cut-off Sigma(F) 2.35
    Number of Reflections(Observed) 175745
    Number of Reflections(R-Free) 7731
    Percent Reflections(Observed) 95.78
    R-Factor(Observed) 0.1751
    R-Work 0.174
    R-Free 0.1994
    R-Free Selection Details Inherited free reflections from 4F2R
     
    Temperature Factor Modeling
    Data Not Available
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6511
    Shell Resolution(Low) 1.6699
    Number of Reflections(R-Free) 120
    Number of Reflections(R-Work) 2414
    R-Factor(R-Work) 0.2834
    R-Factor(R-Free) 0.2956
    Percent Reflections(Observed) 42.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6699
    Shell Resolution(Low) 1.6895
    Number of Reflections(R-Free) 255
    Number of Reflections(R-Work) 5243
    R-Factor(R-Work) 0.2301
    R-Factor(R-Free) 0.2588
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6895
    Shell Resolution(Low) 1.7101
    Number of Reflections(R-Free) 260
    Number of Reflections(R-Work) 5285
    R-Factor(R-Work) 0.2208
    R-Factor(R-Free) 0.2552
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7101
    Shell Resolution(Low) 1.7318
    Number of Reflections(R-Free) 264
    Number of Reflections(R-Work) 5348
    R-Factor(R-Work) 0.2142
    R-Factor(R-Free) 0.2316
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7318
    Shell Resolution(Low) 1.7546
    Number of Reflections(R-Free) 268
    Number of Reflections(R-Work) 5411
    R-Factor(R-Work) 0.2141
    R-Factor(R-Free) 0.2754
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7546
    Shell Resolution(Low) 1.7786
    Number of Reflections(R-Free) 268
    Number of Reflections(R-Work) 5449
    R-Factor(R-Work) 0.2037
    R-Factor(R-Free) 0.2243
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7786
    Shell Resolution(Low) 1.804
    Number of Reflections(R-Free) 283
    Number of Reflections(R-Work) 5493
    R-Factor(R-Work) 0.1971
    R-Factor(R-Free) 0.2233
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.804
    Shell Resolution(Low) 1.8309
    Number of Reflections(R-Free) 283
    Number of Reflections(R-Work) 5485
    R-Factor(R-Work) 0.2042
    R-Factor(R-Free) 0.2304
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8309
    Shell Resolution(Low) 1.8596
    Number of Reflections(R-Free) 276
    Number of Reflections(R-Work) 5566
    R-Factor(R-Work) 0.2002
    R-Factor(R-Free) 0.2372
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8596
    Shell Resolution(Low) 1.89
    Number of Reflections(R-Free) 285
    Number of Reflections(R-Work) 5543
    R-Factor(R-Work) 0.1893
    R-Factor(R-Free) 0.2297
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.89
    Shell Resolution(Low) 1.9226
    Number of Reflections(R-Free) 291
    Number of Reflections(R-Work) 5592
    R-Factor(R-Work) 0.1835
    R-Factor(R-Free) 0.2337
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9226
    Shell Resolution(Low) 1.9576
    Number of Reflections(R-Free) 289
    Number of Reflections(R-Work) 5668
    R-Factor(R-Work) 0.1818
    R-Factor(R-Free) 0.2156
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9576
    Shell Resolution(Low) 1.9952
    Number of Reflections(R-Free) 199
    Number of Reflections(R-Work) 5759
    R-Factor(R-Work) 0.1757
    R-Factor(R-Free) 0.1902
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9952
    Shell Resolution(Low) 2.036
    Number of Reflections(R-Free) 207
    Number of Reflections(R-Work) 5790
    R-Factor(R-Work) 0.1735
    R-Factor(R-Free) 0.2173
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.036
    Shell Resolution(Low) 2.0802
    Number of Reflections(R-Free) 210
    Number of Reflections(R-Work) 5776
    R-Factor(R-Work) 0.1718
    R-Factor(R-Free) 0.1852
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0802
    Shell Resolution(Low) 2.1286
    Number of Reflections(R-Free) 234
    Number of Reflections(R-Work) 5818
    R-Factor(R-Work) 0.1686
    R-Factor(R-Free) 0.2093
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1286
    Shell Resolution(Low) 2.1818
    Number of Reflections(R-Free) 223
    Number of Reflections(R-Work) 5812
    R-Factor(R-Work) 0.1644
    R-Factor(R-Free) 0.1945
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1818
    Shell Resolution(Low) 2.2408
    Number of Reflections(R-Free) 273
    Number of Reflections(R-Work) 5771
    R-Factor(R-Work) 0.1658
    R-Factor(R-Free) 0.1947
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2408
    Shell Resolution(Low) 2.3067
    Number of Reflections(R-Free) 213
    Number of Reflections(R-Work) 5882
    R-Factor(R-Work) 0.1589
    R-Factor(R-Free) 0.2018
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3067
    Shell Resolution(Low) 2.3812
    Number of Reflections(R-Free) 229
    Number of Reflections(R-Work) 5821
    R-Factor(R-Work) 0.1594
    R-Factor(R-Free) 0.1912
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3812
    Shell Resolution(Low) 2.4662
    Number of Reflections(R-Free) 245
    Number of Reflections(R-Work) 5850
    R-Factor(R-Work) 0.1635
    R-Factor(R-Free) 0.1971
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4662
    Shell Resolution(Low) 2.565
    Number of Reflections(R-Free) 232
    Number of Reflections(R-Work) 5877
    R-Factor(R-Work) 0.1662
    R-Factor(R-Free) 0.1846
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.565
    Shell Resolution(Low) 2.6817
    Number of Reflections(R-Free) 252
    Number of Reflections(R-Work) 5835
    R-Factor(R-Work) 0.1743
    R-Factor(R-Free) 0.1945
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6817
    Shell Resolution(Low) 2.823
    Number of Reflections(R-Free) 258
    Number of Reflections(R-Work) 5871
    R-Factor(R-Work) 0.1812
    R-Factor(R-Free) 0.2224
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.823
    Shell Resolution(Low) 2.9997
    Number of Reflections(R-Free) 287
    Number of Reflections(R-Work) 5877
    R-Factor(R-Work) 0.1861
    R-Factor(R-Free) 0.2255
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9997
    Shell Resolution(Low) 3.2312
    Number of Reflections(R-Free) 294
    Number of Reflections(R-Work) 5855
    R-Factor(R-Work) 0.1826
    R-Factor(R-Free) 0.1961
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2312
    Shell Resolution(Low) 3.5561
    Number of Reflections(R-Free) 306
    Number of Reflections(R-Work) 5866
    R-Factor(R-Work) 0.1662
    R-Factor(R-Free) 0.1898
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5561
    Shell Resolution(Low) 4.0699
    Number of Reflections(R-Free) 299
    Number of Reflections(R-Work) 5933
    R-Factor(R-Work) 0.1541
    R-Factor(R-Free) 0.1683
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0699
    Shell Resolution(Low) 5.1249
    Number of Reflections(R-Free) 312
    Number of Reflections(R-Work) 5952
    R-Factor(R-Work) 0.1464
    R-Factor(R-Free) 0.1685
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1249
    Shell Resolution(Low) 34.1972
    Number of Reflections(R-Free) 316
    Number of Reflections(R-Work) 6172
    R-Factor(R-Work) 0.1918
    R-Factor(R-Free) 0.2018
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 15.293
    f_plane_restr 0.007
    f_chiral_restr 0.094
    f_angle_d 1.403
    f_bond_d 0.011
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 9310
    Nucleic Acid Atoms 832
    Heterogen Atoms 110
    Solvent Atoms 1323
     
     
  •   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