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X-RAY DIFFRACTION
Materials and Methods page
4EZ9
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5.8
    Temperature 290.0
    Details 48%-53% 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 = 93.92 α = 90
    b = 108.96 β = 90
    c = 149.49 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2010-04-22
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ALS BEAMLINE 12.3.1
    Wavelength List 0.9795
    Site ALS
    Beamline 12.3.1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.64
    Resolution(Low) 50
    Number Reflections(Observed) 171000
    Percent Possible(Observed) 91.2
    R Merge I(Observed) 0.042
    B(Isotropic) From Wilson Plot 28.337
    Redundancy 5.6
     
    High Resolution Shell Details
    Resolution(High) 1.64
    Resolution(Low) 1.74
    Percent Possible(All) 99.9
    R Merge I(Observed) 0.496
    Mean I Over Sigma(Observed) 3.85
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 1.64
    Resolution(Low) 43.125
    Cut-off Sigma(F) 2.35
    Number of Reflections(Observed) 161679
    Number of Reflections(R-Free) 7358
    Percent Reflections(Observed) 86.23
    R-Factor(Observed) 0.1691
    R-Work 0.168
    R-Free 0.1909
     
    Temperature Factor Modeling
    Data Not Available
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.64
    Shell Resolution(Low) 1.6586
    Number of Reflections(R-Free) 269
    Number of Reflections(R-Work) 5124
    R-Factor(R-Work) 0.2138
    R-Factor(R-Free) 0.2329
    Percent Reflections(Observed) 86.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6586
    Shell Resolution(Low) 1.6782
    Number of Reflections(R-Free) 271
    Number of Reflections(R-Work) 5144
    R-Factor(R-Work) 0.2101
    R-Factor(R-Free) 0.2591
    Percent Reflections(Observed) 88.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6782
    Shell Resolution(Low) 1.6986
    Number of Reflections(R-Free) 274
    Number of Reflections(R-Work) 5200
    R-Factor(R-Work) 0.2031
    R-Factor(R-Free) 0.244
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6986
    Shell Resolution(Low) 1.7201
    Number of Reflections(R-Free) 277
    Number of Reflections(R-Work) 5270
    R-Factor(R-Work) 0.1992
    R-Factor(R-Free) 0.2502
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7201
    Shell Resolution(Low) 1.7428
    Number of Reflections(R-Free) 282
    Number of Reflections(R-Work) 5349
    R-Factor(R-Work) 0.1897
    R-Factor(R-Free) 0.235
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7428
    Shell Resolution(Low) 1.7666
    Number of Reflections(R-Free) 279
    Number of Reflections(R-Work) 5300
    R-Factor(R-Work) 0.1829
    R-Factor(R-Free) 0.2106
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7666
    Shell Resolution(Low) 1.7919
    Number of Reflections(R-Free) 284
    Number of Reflections(R-Work) 5394
    R-Factor(R-Work) 0.178
    R-Factor(R-Free) 0.2206
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7919
    Shell Resolution(Low) 1.8186
    Number of Reflections(R-Free) 286
    Number of Reflections(R-Work) 5449
    R-Factor(R-Work) 0.1761
    R-Factor(R-Free) 0.216
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8186
    Shell Resolution(Low) 1.847
    Number of Reflections(R-Free) 285
    Number of Reflections(R-Work) 5415
    R-Factor(R-Work) 0.1767
    R-Factor(R-Free) 0.2061
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.847
    Shell Resolution(Low) 1.8773
    Number of Reflections(R-Free) 276
    Number of Reflections(R-Work) 5241
    R-Factor(R-Work) 0.1727
    R-Factor(R-Free) 0.2233
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8773
    Shell Resolution(Low) 1.9097
    Number of Reflections(R-Free) 115
    Number of Reflections(R-Work) 2181
    R-Factor(R-Work) 0.178
    R-Factor(R-Free) 0.2301
    Percent Reflections(Observed) 77.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9097
    Shell Resolution(Low) 1.9444
    Number of Reflections(R-Free) 1
    Number of Reflections(R-Work) 8
    R-Factor(R-Work) 0.1339
    R-Factor(R-Free) 0.1035
    Percent Reflections(Observed) 19.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9444
    Shell Resolution(Low) 1.9818
    Number of Reflections(R-Free) 263
    Number of Reflections(R-Work) 5003
    R-Factor(R-Work) 0.1812
    R-Factor(R-Free) 0.2226
    Percent Reflections(Observed) 85.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9818
    Shell Resolution(Low) 2.0223
    Number of Reflections(R-Free) 219
    Number of Reflections(R-Work) 5762
    R-Factor(R-Work) 0.1705
    R-Factor(R-Free) 0.1902
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0223
    Shell Resolution(Low) 2.0662
    Number of Reflections(R-Free) 211
    Number of Reflections(R-Work) 5796
    R-Factor(R-Work) 0.1638
    R-Factor(R-Free) 0.1843
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0662
    Shell Resolution(Low) 2.1143
    Number of Reflections(R-Free) 233
    Number of Reflections(R-Work) 5854
    R-Factor(R-Work) 0.1623
    R-Factor(R-Free) 0.1877
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1143
    Shell Resolution(Low) 2.1672
    Number of Reflections(R-Free) 228
    Number of Reflections(R-Work) 5829
    R-Factor(R-Work) 0.1618
    R-Factor(R-Free) 0.1881
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1672
    Shell Resolution(Low) 2.2258
    Number of Reflections(R-Free) 262
    Number of Reflections(R-Work) 5270
    R-Factor(R-Work) 0.1688
    R-Factor(R-Free) 0.2104
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2258
    Shell Resolution(Low) 2.2913
    Number of Reflections(R-Free) 39
    Number of Reflections(R-Work) 1107
    R-Factor(R-Work) 0.1737
    R-Factor(R-Free) 0.2276
    Percent Reflections(Observed) 81.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2913
    Shell Resolution(Low) 2.3652
    Number of Reflections(R-Free) 224
    Number of Reflections(R-Work) 5775
    R-Factor(R-Work) 0.1565
    R-Factor(R-Free) 0.1833
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3652
    Shell Resolution(Low) 2.4497
    Number of Reflections(R-Free) 234
    Number of Reflections(R-Work) 5877
    R-Factor(R-Work) 0.1573
    R-Factor(R-Free) 0.1935
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4497
    Shell Resolution(Low) 2.5478
    Number of Reflections(R-Free) 245
    Number of Reflections(R-Work) 5886
    R-Factor(R-Work) 0.1572
    R-Factor(R-Free) 0.1683
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5478
    Shell Resolution(Low) 2.6637
    Number of Reflections(R-Free) 251
    Number of Reflections(R-Work) 5896
    R-Factor(R-Work) 0.1633
    R-Factor(R-Free) 0.1732
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6637
    Shell Resolution(Low) 2.8042
    Number of Reflections(R-Free) 256
    Number of Reflections(R-Work) 5880
    R-Factor(R-Work) 0.1707
    R-Factor(R-Free) 0.1835
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8042
    Shell Resolution(Low) 2.9798
    Number of Reflections(R-Free) 278
    Number of Reflections(R-Work) 5873
    R-Factor(R-Work) 0.1698
    R-Factor(R-Free) 0.1978
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9798
    Shell Resolution(Low) 3.2098
    Number of Reflections(R-Free) 292
    Number of Reflections(R-Work) 5943
    R-Factor(R-Work) 0.1721
    R-Factor(R-Free) 0.1906
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2098
    Shell Resolution(Low) 3.5327
    Number of Reflections(R-Free) 312
    Number of Reflections(R-Work) 5875
    R-Factor(R-Work) 0.1611
    R-Factor(R-Free) 0.1731
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5327
    Shell Resolution(Low) 4.0436
    Number of Reflections(R-Free) 299
    Number of Reflections(R-Work) 5855
    R-Factor(R-Work) 0.1645
    R-Factor(R-Free) 0.1866
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0436
    Shell Resolution(Low) 5.0932
    Number of Reflections(R-Free) 309
    Number of Reflections(R-Work) 5944
    R-Factor(R-Work) 0.139
    R-Factor(R-Free) 0.1627
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0932
    Shell Resolution(Low) 43.1402
    Number of Reflections(R-Free) 304
    Number of Reflections(R-Work) 5821
    R-Factor(R-Work) 0.1961
    R-Factor(R-Free) 0.1964
    Percent Reflections(Observed) 92.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.007
    f_chiral_restr 0.077
    f_dihedral_angle_d 15.327
    f_angle_d 1.348
    f_bond_d 0.01
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 9280
    Nucleic Acid Atoms 828
    Heterogen Atoms 46
    Solvent Atoms 1363
     
     
  •   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