POP-OUT | CLOSE

An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3PA2
  •   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 = 65.27 α = 90
    b = 79.13 β = 100.27
    c = 69.07 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 2010-08-08
     
    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) 29.08
    Number Reflections(All) 114707
    Number Reflections(Observed) 114707
    Percent Possible(Observed) 99.7
    Redundancy 3.7
     
    High Resolution Shell Details
    Resolution(High) 1.48
    Resolution(Low) 1.52
    Percent Possible(All) 99.8
    Mean I Over Sigma(Observed) 2.4
    R-Sym I(Observed) 0.647
    Redundancy 3.7
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.48
    Resolution(Low) 29.08
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 114698
    Number of Reflections(Observed) 114698
    Number of Reflections(R-Free) 5772
    Percent Reflections(Observed) 99.78
    R-Factor(Observed) 0.1857
    R-Work 0.1848
    R-Free 0.2038
     
    Temperature Factor Modeling
    Isotropic Thermal Model Isotropic, TLS
    Anisotropic B[1][1] -0.351
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -2.9715
    Anisotropic B[2][2] -1.1312
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 1.4822
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.48
    Shell Resolution(Low) 1.4968
    Number of Reflections(R-Free) 203
    Number of Reflections(R-Work) 3590
    R-Factor(R-Work) 0.2892
    R-Factor(R-Free) 0.296
    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) 202
    Number of Reflections(R-Work) 3605
    R-Factor(R-Work) 0.2796
    R-Factor(R-Free) 0.2895
    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) 194
    Number of Reflections(R-Work) 3608
    R-Factor(R-Work) 0.2684
    R-Factor(R-Free) 0.326
    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) 186
    Number of Reflections(R-Work) 3652
    R-Factor(R-Work) 0.2532
    R-Factor(R-Free) 0.2527
    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) 191
    Number of Reflections(R-Work) 3579
    R-Factor(R-Work) 0.2452
    R-Factor(R-Free) 0.2503
    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) 174
    Number of Reflections(R-Work) 3652
    R-Factor(R-Work) 0.2323
    R-Factor(R-Free) 0.2761
    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) 212
    Number of Reflections(R-Work) 3573
    R-Factor(R-Work) 0.2347
    R-Factor(R-Free) 0.2733
    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) 191
    Number of Reflections(R-Work) 3664
    R-Factor(R-Work) 0.2231
    R-Factor(R-Free) 0.2486
    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) 211
    Number of Reflections(R-Work) 3585
    R-Factor(R-Work) 0.2161
    R-Factor(R-Free) 0.2369
    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) 192
    Number of Reflections(R-Work) 3645
    R-Factor(R-Work) 0.2034
    R-Factor(R-Free) 0.2471
    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) 188
    Number of Reflections(R-Work) 3631
    R-Factor(R-Work) 0.2012
    R-Factor(R-Free) 0.2015
    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) 167
    Number of Reflections(R-Work) 3625
    R-Factor(R-Work) 0.1897
    R-Factor(R-Free) 0.2188
    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) 200
    Number of Reflections(R-Work) 3613
    R-Factor(R-Work) 0.1814
    R-Factor(R-Free) 0.2081
    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) 194
    Number of Reflections(R-Work) 3616
    R-Factor(R-Work) 0.1824
    R-Factor(R-Free) 0.2073
    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) 198
    Number of Reflections(R-Work) 3662
    R-Factor(R-Work) 0.1781
    R-Factor(R-Free) 0.2015
    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) 190
    Number of Reflections(R-Work) 3598
    R-Factor(R-Work) 0.1779
    R-Factor(R-Free) 0.2301
    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) 210
    Number of Reflections(R-Work) 3603
    R-Factor(R-Work) 0.1765
    R-Factor(R-Free) 0.1865
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9557
    Shell Resolution(Low) 2.0085
    Number of Reflections(R-Free) 197
    Number of Reflections(R-Work) 3648
    R-Factor(R-Work) 0.1759
    R-Factor(R-Free) 0.1936
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0085
    Shell Resolution(Low) 2.0676
    Number of Reflections(R-Free) 177
    Number of Reflections(R-Work) 3634
    R-Factor(R-Work) 0.1787
    R-Factor(R-Free) 0.1997
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0676
    Shell Resolution(Low) 2.1343
    Number of Reflections(R-Free) 178
    Number of Reflections(R-Work) 3665
    R-Factor(R-Work) 0.1791
    R-Factor(R-Free) 0.2311
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1343
    Shell Resolution(Low) 2.2106
    Number of Reflections(R-Free) 194
    Number of Reflections(R-Work) 3612
    R-Factor(R-Work) 0.176
    R-Factor(R-Free) 0.1834
    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) 208
    Number of Reflections(R-Work) 3620
    R-Factor(R-Work) 0.1747
    R-Factor(R-Free) 0.1878
    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) 214
    Number of Reflections(R-Work) 3617
    R-Factor(R-Work) 0.1736
    R-Factor(R-Free) 0.198
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4037
    Shell Resolution(Low) 2.5303
    Number of Reflections(R-Free) 191
    Number of Reflections(R-Work) 3621
    R-Factor(R-Work) 0.1773
    R-Factor(R-Free) 0.1946
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5303
    Shell Resolution(Low) 2.6888
    Number of Reflections(R-Free) 180
    Number of Reflections(R-Work) 3652
    R-Factor(R-Work) 0.1839
    R-Factor(R-Free) 0.2024
    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) 195
    Number of Reflections(R-Work) 3642
    R-Factor(R-Work) 0.1829
    R-Factor(R-Free) 0.2056
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8962
    Shell Resolution(Low) 3.1873
    Number of Reflections(R-Free) 172
    Number of Reflections(R-Work) 3668
    R-Factor(R-Work) 0.1755
    R-Factor(R-Free) 0.1924
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1873
    Shell Resolution(Low) 3.6478
    Number of Reflections(R-Free) 189
    Number of Reflections(R-Work) 3675
    R-Factor(R-Work) 0.1723
    R-Factor(R-Free) 0.1938
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6478
    Shell Resolution(Low) 4.5929
    Number of Reflections(R-Free) 206
    Number of Reflections(R-Work) 3628
    R-Factor(R-Work) 0.154
    R-Factor(R-Free) 0.1641
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5929
    Shell Resolution(Low) 29.0855
    Number of Reflections(R-Free) 168
    Number of Reflections(R-Work) 3743
    R-Factor(R-Work) 0.1836
    R-Factor(R-Free) 0.186
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.006
    f_chiral_restr 0.075
    f_dihedral_angle_d 14.799
    f_angle_d 1.12
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4823
    Nucleic Acid Atoms 0
    Heterogen Atoms 139
    Solvent Atoms 765
     
     
  •   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