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X-RAY DIFFRACTION
Materials and Methods page
3PA1
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.5
    Temperature 293.0
    Details 0.1 M Imidazol, 8.25% (w/v) PEG 8000, 1% (v/v) MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 65.19 α = 90
    b = 78.99 β = 101.06
    c = 70.1 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 95
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 225 mm CCD
    Collection Date 2010-04-08
     
    Diffraction Radiation
    Monochromator Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 22-BM
    Wavelength List 1.0
    Site APS
    Beamline 22-BM
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) -3.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.48
    Resolution(Low) 29.65
    Number Reflections(Observed) 115874
    Percent Possible(Observed) 99.8
    Redundancy 3.8
     
    High Resolution Shell Details
    Resolution(High) 1.48
    Resolution(Low) 1.52
    Percent Possible(All) 99.8
    Mean I Over Sigma(Observed) 12.5
    R-Sym I(Observed) 0.657
    Redundancy 3.8
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.48
    Resolution(Low) 29.652
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 115862
    Number of Reflections(Observed) 115862
    Number of Reflections(R-Free) 5840
    Percent Reflections(Observed) 99.87
    R-Factor(Observed) 0.1786
    R-Work 0.1776
    R-Free 0.1982
     
    Temperature Factor Modeling
    Isotropic Thermal Model isotropic, TLS
    Anisotropic B[1][1] -0.9853
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -4.1005
    Anisotropic B[2][2] -0.8204
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 1.8057
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.48
    Shell Resolution(Low) 1.4968
    Number of Reflections(R-Free) 197
    Number of Reflections(R-Work) 3622
    R-Factor(R-Work) 0.2905
    R-Factor(R-Free) 0.3028
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4968
    Shell Resolution(Low) 1.5144
    Number of Reflections(R-Free) 219
    Number of Reflections(R-Work) 3627
    R-Factor(R-Work) 0.2819
    R-Factor(R-Free) 0.315
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5144
    Shell Resolution(Low) 1.5329
    Number of Reflections(R-Free) 189
    Number of Reflections(R-Work) 3646
    R-Factor(R-Work) 0.2697
    R-Factor(R-Free) 0.3048
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5329
    Shell Resolution(Low) 1.5523
    Number of Reflections(R-Free) 212
    Number of Reflections(R-Work) 3697
    R-Factor(R-Work) 0.2567
    R-Factor(R-Free) 0.2761
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5523
    Shell Resolution(Low) 1.5727
    Number of Reflections(R-Free) 164
    Number of Reflections(R-Work) 3631
    R-Factor(R-Work) 0.2427
    R-Factor(R-Free) 0.2645
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5727
    Shell Resolution(Low) 1.5943
    Number of Reflections(R-Free) 173
    Number of Reflections(R-Work) 3709
    R-Factor(R-Work) 0.2328
    R-Factor(R-Free) 0.2364
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5943
    Shell Resolution(Low) 1.617
    Number of Reflections(R-Free) 226
    Number of Reflections(R-Work) 3609
    R-Factor(R-Work) 0.2266
    R-Factor(R-Free) 0.2473
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.617
    Shell Resolution(Low) 1.6412
    Number of Reflections(R-Free) 195
    Number of Reflections(R-Work) 3633
    R-Factor(R-Work) 0.2175
    R-Factor(R-Free) 0.2657
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6412
    Shell Resolution(Low) 1.6668
    Number of Reflections(R-Free) 206
    Number of Reflections(R-Work) 3666
    R-Factor(R-Work) 0.2124
    R-Factor(R-Free) 0.236
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6668
    Shell Resolution(Low) 1.6941
    Number of Reflections(R-Free) 203
    Number of Reflections(R-Work) 3652
    R-Factor(R-Work) 0.2059
    R-Factor(R-Free) 0.2336
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6941
    Shell Resolution(Low) 1.7234
    Number of Reflections(R-Free) 181
    Number of Reflections(R-Work) 3665
    R-Factor(R-Work) 0.1986
    R-Factor(R-Free) 0.2207
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7234
    Shell Resolution(Low) 1.7547
    Number of Reflections(R-Free) 180
    Number of Reflections(R-Work) 3700
    R-Factor(R-Work) 0.1932
    R-Factor(R-Free) 0.2345
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7547
    Shell Resolution(Low) 1.7884
    Number of Reflections(R-Free) 182
    Number of Reflections(R-Work) 3634
    R-Factor(R-Work) 0.1731
    R-Factor(R-Free) 0.1801
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7884
    Shell Resolution(Low) 1.8249
    Number of Reflections(R-Free) 215
    Number of Reflections(R-Work) 3658
    R-Factor(R-Work) 0.1688
    R-Factor(R-Free) 0.1934
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8249
    Shell Resolution(Low) 1.8646
    Number of Reflections(R-Free) 205
    Number of Reflections(R-Work) 3632
    R-Factor(R-Work) 0.1604
    R-Factor(R-Free) 0.1579
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8646
    Shell Resolution(Low) 1.908
    Number of Reflections(R-Free) 191
    Number of Reflections(R-Work) 3670
    R-Factor(R-Work) 0.165
    R-Factor(R-Free) 0.2129
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.908
    Shell Resolution(Low) 1.9557
    Number of Reflections(R-Free) 208
    Number of Reflections(R-Work) 3659
    R-Factor(R-Work) 0.1652
    R-Factor(R-Free) 0.1865
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9557
    Shell Resolution(Low) 2.0086
    Number of Reflections(R-Free) 192
    Number of Reflections(R-Work) 3685
    R-Factor(R-Work) 0.1673
    R-Factor(R-Free) 0.1957
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0086
    Shell Resolution(Low) 2.0676
    Number of Reflections(R-Free) 185
    Number of Reflections(R-Work) 3660
    R-Factor(R-Work) 0.1729
    R-Factor(R-Free) 0.2055
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0676
    Shell Resolution(Low) 2.1344
    Number of Reflections(R-Free) 174
    Number of Reflections(R-Work) 3683
    R-Factor(R-Work) 0.1711
    R-Factor(R-Free) 0.1844
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1344
    Shell Resolution(Low) 2.2106
    Number of Reflections(R-Free) 195
    Number of Reflections(R-Work) 3657
    R-Factor(R-Work) 0.1678
    R-Factor(R-Free) 0.2012
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2106
    Shell Resolution(Low) 2.2991
    Number of Reflections(R-Free) 206
    Number of Reflections(R-Work) 3651
    R-Factor(R-Work) 0.166
    R-Factor(R-Free) 0.1893
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2991
    Shell Resolution(Low) 2.4037
    Number of Reflections(R-Free) 216
    Number of Reflections(R-Work) 3667
    R-Factor(R-Work) 0.1611
    R-Factor(R-Free) 0.1815
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4037
    Shell Resolution(Low) 2.5304
    Number of Reflections(R-Free) 198
    Number of Reflections(R-Work) 3679
    R-Factor(R-Work) 0.1637
    R-Factor(R-Free) 0.1778
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5304
    Shell Resolution(Low) 2.6888
    Number of Reflections(R-Free) 185
    Number of Reflections(R-Work) 3679
    R-Factor(R-Work) 0.1714
    R-Factor(R-Free) 0.2083
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6888
    Shell Resolution(Low) 2.8962
    Number of Reflections(R-Free) 188
    Number of Reflections(R-Work) 3667
    R-Factor(R-Work) 0.1754
    R-Factor(R-Free) 0.1855
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8962
    Shell Resolution(Low) 3.1874
    Number of Reflections(R-Free) 180
    Number of Reflections(R-Work) 3723
    R-Factor(R-Work) 0.1734
    R-Factor(R-Free) 0.186
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1874
    Shell Resolution(Low) 3.6479
    Number of Reflections(R-Free) 194
    Number of Reflections(R-Work) 3689
    R-Factor(R-Work) 0.1654
    R-Factor(R-Free) 0.1863
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6479
    Shell Resolution(Low) 4.5932
    Number of Reflections(R-Free) 209
    Number of Reflections(R-Work) 3687
    R-Factor(R-Work) 0.1466
    R-Factor(R-Free) 0.1672
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5932
    Shell Resolution(Low) 29.6575
    Number of Reflections(R-Free) 172
    Number of Reflections(R-Work) 3785
    R-Factor(R-Work) 0.1822
    R-Factor(R-Free) 0.192
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.006
    f_chiral_restr 0.08
    f_dihedral_angle_d 13.844
    f_angle_d 1.155
    f_bond_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4864
    Nucleic Acid Atoms 0
    Heterogen Atoms 106
    Solvent Atoms 777
     
     
  •   Software and Computing Hide
    Computing
    Data Collection SERGUI
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution PHASER (2.1.4)
    Structure Refinement PHENIX (phenix.refine: 1.6.4_486)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.6.4_486)
    model building PHASER version: (2.1.4)
    data collection SERGUI