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X-RAY DIFFRACTION
Materials and Methods page
4F3O
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5.8
    Temperature 290.0
    Details 49%-51% 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 = 93.83 α = 90
    b = 109.33 β = 90
    c = 150.11 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2012-03-03
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ALS BEAMLINE 12.3.1
    Wavelength List 1.1158
    Site ALS
    Beamline 12.3.1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.57
    Resolution(Low) 100
    Number Reflections(Observed) 199455
    Percent Possible(Observed) 92.9
    R Merge I(Observed) 0.048
    B(Isotropic) From Wilson Plot 27.766
    Redundancy 8.6
     
    High Resolution Shell Details
    Resolution(High) 1.57
    Resolution(Low) 1.66
    Percent Possible(All) 99.9
    R Merge I(Observed) 0.462
    Mean I Over Sigma(Observed) 3.75
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 1.57
    Resolution(Low) 79.565
    Cut-off Sigma(F) 2.35
    Number of Reflections(Observed) 191796
    Number of Reflections(R-Free) 8791
    Percent Reflections(Observed) 89.3
    R-Factor(Observed) 0.1803
    R-Work 0.1792
    R-Free 0.2036
    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) 1.57
    Shell Resolution(Low) 1.5878
    Number of Reflections(R-Free) 305
    Number of Reflections(R-Work) 5800
    R-Factor(R-Work) 0.258
    R-Factor(R-Free) 0.2784
    Percent Reflections(Observed) 86.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5878
    Shell Resolution(Low) 1.6065
    Number of Reflections(R-Free) 315
    Number of Reflections(R-Work) 5984
    R-Factor(R-Work) 0.2379
    R-Factor(R-Free) 0.2388
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6065
    Shell Resolution(Low) 1.6261
    Number of Reflections(R-Free) 316
    Number of Reflections(R-Work) 5999
    R-Factor(R-Work) 0.2265
    R-Factor(R-Free) 0.2589
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6261
    Shell Resolution(Low) 1.6467
    Number of Reflections(R-Free) 324
    Number of Reflections(R-Work) 6161
    R-Factor(R-Work) 0.2223
    R-Factor(R-Free) 0.2392
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6467
    Shell Resolution(Low) 1.6684
    Number of Reflections(R-Free) 325
    Number of Reflections(R-Work) 6178
    R-Factor(R-Work) 0.2171
    R-Factor(R-Free) 0.249
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6684
    Shell Resolution(Low) 1.6912
    Number of Reflections(R-Free) 329
    Number of Reflections(R-Work) 6254
    R-Factor(R-Work) 0.2107
    R-Factor(R-Free) 0.2424
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6912
    Shell Resolution(Low) 1.7154
    Number of Reflections(R-Free) 333
    Number of Reflections(R-Work) 6324
    R-Factor(R-Work) 0.2112
    R-Factor(R-Free) 0.2454
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7154
    Shell Resolution(Low) 1.741
    Number of Reflections(R-Free) 335
    Number of Reflections(R-Work) 6358
    R-Factor(R-Work) 0.2069
    R-Factor(R-Free) 0.2446
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.741
    Shell Resolution(Low) 1.7682
    Number of Reflections(R-Free) 338
    Number of Reflections(R-Work) 6423
    R-Factor(R-Work) 0.2009
    R-Factor(R-Free) 0.2199
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7682
    Shell Resolution(Low) 1.7972
    Number of Reflections(R-Free) 337
    Number of Reflections(R-Work) 6417
    R-Factor(R-Work) 0.1891
    R-Factor(R-Free) 0.2142
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7972
    Shell Resolution(Low) 1.8282
    Number of Reflections(R-Free) 342
    Number of Reflections(R-Work) 6482
    R-Factor(R-Work) 0.1874
    R-Factor(R-Free) 0.2263
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8282
    Shell Resolution(Low) 1.8614
    Number of Reflections(R-Free) 340
    Number of Reflections(R-Work) 6464
    R-Factor(R-Work) 0.187
    R-Factor(R-Free) 0.2248
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8614
    Shell Resolution(Low) 1.8972
    Number of Reflections(R-Free) 273
    Number of Reflections(R-Work) 5187
    R-Factor(R-Work) 0.1859
    R-Factor(R-Free) 0.2171
    Percent Reflections(Observed) 83.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.936
    Shell Resolution(Low) 1.9781
    Number of Reflections(R-Free) 263
    Number of Reflections(R-Work) 5010
    R-Factor(R-Work) 0.1834
    R-Factor(R-Free) 0.2319
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9781
    Shell Resolution(Low) 2.0241
    Number of Reflections(R-Free) 256
    Number of Reflections(R-Work) 6767
    R-Factor(R-Work) 0.1779
    R-Factor(R-Free) 0.213
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0241
    Shell Resolution(Low) 2.0747
    Number of Reflections(R-Free) 239
    Number of Reflections(R-Work) 6775
    R-Factor(R-Work) 0.1691
    R-Factor(R-Free) 0.175
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0747
    Shell Resolution(Low) 2.1308
    Number of Reflections(R-Free) 271
    Number of Reflections(R-Work) 6835
    R-Factor(R-Work) 0.1688
    R-Factor(R-Free) 0.1882
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1308
    Shell Resolution(Low) 2.1935
    Number of Reflections(R-Free) 271
    Number of Reflections(R-Work) 6775
    R-Factor(R-Work) 0.1688
    R-Factor(R-Free) 0.1962
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1935
    Shell Resolution(Low) 2.2643
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2901
    R-Factor(R-Work) 0.1673
    R-Factor(R-Free) 0.191
    Percent Reflections(Observed) 88.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2643
    Shell Resolution(Low) 2.3453
    Number of Reflections(R-Free) 215
    Number of Reflections(R-Work) 5705
    R-Factor(R-Work) 0.1677
    R-Factor(R-Free) 0.2016
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3453
    Shell Resolution(Low) 2.4392
    Number of Reflections(R-Free) 273
    Number of Reflections(R-Work) 6826
    R-Factor(R-Work) 0.1692
    R-Factor(R-Free) 0.1926
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4392
    Shell Resolution(Low) 2.5502
    Number of Reflections(R-Free) 280
    Number of Reflections(R-Work) 6834
    R-Factor(R-Work) 0.1681
    R-Factor(R-Free) 0.1848
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5502
    Shell Resolution(Low) 2.6846
    Number of Reflections(R-Free) 286
    Number of Reflections(R-Work) 6898
    R-Factor(R-Work) 0.1766
    R-Factor(R-Free) 0.2053
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6846
    Shell Resolution(Low) 2.8528
    Number of Reflections(R-Free) 307
    Number of Reflections(R-Work) 6862
    R-Factor(R-Work) 0.1851
    R-Factor(R-Free) 0.2195
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8528
    Shell Resolution(Low) 3.0731
    Number of Reflections(R-Free) 331
    Number of Reflections(R-Work) 6844
    R-Factor(R-Work) 0.1858
    R-Factor(R-Free) 0.2198
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0731
    Shell Resolution(Low) 3.3824
    Number of Reflections(R-Free) 356
    Number of Reflections(R-Work) 6871
    R-Factor(R-Work) 0.1745
    R-Factor(R-Free) 0.1977
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3824
    Shell Resolution(Low) 3.8718
    Number of Reflections(R-Free) 345
    Number of Reflections(R-Work) 6918
    R-Factor(R-Work) 0.164
    R-Factor(R-Free) 0.1866
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8718
    Shell Resolution(Low) 4.878
    Number of Reflections(R-Free) 365
    Number of Reflections(R-Work) 6950
    R-Factor(R-Work) 0.1513
    R-Factor(R-Free) 0.1806
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.878
    Shell Resolution(Low) 79.6673
    Number of Reflections(R-Free) 370
    Number of Reflections(R-Work) 7203
    R-Factor(R-Work) 0.2005
    R-Factor(R-Free) 0.1987
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 15.236
    f_plane_restr 0.007
    f_chiral_restr 0.076
    f_angle_d 1.357
    f_bond_d 0.01
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 9185
    Nucleic Acid Atoms 850
    Heterogen Atoms 58
    Solvent Atoms 1365
     
     
  •   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