POP-OUT | CLOSE
 
X-RAY DIFFRACTION
Materials and Methods page
4I0X
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5.6
    Temperature 291.0
    Details RESERVOIR: 0.1M tri-sodium citrate, pH5.6, 0.2M potassium sodium tartrate, 2M ammonium sulfate. PROTEIN CONCENTRATION: 11 MG/ML. PROTEIN BUFFER: 20 mM Tris, pH 8.0, 150mM NaCl, 10% Glycerol, 2 mM B-ME. CRYO: reservoir solution plus 25% glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 47.6 α = 114.57
    b = 74.06 β = 103.28
    c = 84.42 γ = 95.52
     
    Space Group
    Space Group Name:    P 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector PIXEL
    Type PSI PILATUS 6M
    Collection Date 2011-07-25
     
    Diffraction Radiation
    Monochromator CRYO-COOLED SI(111) DOUBLE CRYSTAL
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 24-ID-C
    Wavelength List 0.9791
    Site APS
    Beamline 24-ID-C
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 1.96
    Resolution(Low) 20
    Number Reflections(All) 72126
    Number Reflections(Observed) 67097
    Percent Possible(Observed) 93.0
    R Merge I(Observed) 0.057
    Redundancy 1.959
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.956
    Resolution(Low) 19.995
    Cut-off Sigma(F) 1.99
    Number of Reflections(all) 72126
    Number of Reflections(Observed) 67097
    Number of Reflections(R-Free) 6709
    Percent Reflections(Observed) 93.37
    R-Factor(Observed) 0.1647
    R-Work 0.1593
    R-Free 0.2131
     
    Temperature Factor Modeling
    Data Not Available
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9563
    Shell Resolution(Low) 1.9785
    Number of Reflections(R-Free) 205
    Number of Reflections(R-Work) 1838
    R-Factor(R-Work) 0.266
    R-Factor(R-Free) 0.3333
    Percent Reflections(Observed) 85.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9785
    Shell Resolution(Low) 2.0017
    Number of Reflections(R-Free) 228
    Number of Reflections(R-Work) 2059
    R-Factor(R-Work) 0.2287
    R-Factor(R-Free) 0.2684
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0017
    Shell Resolution(Low) 2.0261
    Number of Reflections(R-Free) 218
    Number of Reflections(R-Work) 1962
    R-Factor(R-Work) 0.2128
    R-Factor(R-Free) 0.2655
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0261
    Shell Resolution(Low) 2.0518
    Number of Reflections(R-Free) 234
    Number of Reflections(R-Work) 2098
    R-Factor(R-Work) 0.1976
    R-Factor(R-Free) 0.2558
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0518
    Shell Resolution(Low) 2.0787
    Number of Reflections(R-Free) 221
    Number of Reflections(R-Work) 1994
    R-Factor(R-Work) 0.1911
    R-Factor(R-Free) 0.2662
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0787
    Shell Resolution(Low) 2.1072
    Number of Reflections(R-Free) 227
    Number of Reflections(R-Work) 2052
    R-Factor(R-Work) 0.1911
    R-Factor(R-Free) 0.2574
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1072
    Shell Resolution(Low) 2.1372
    Number of Reflections(R-Free) 225
    Number of Reflections(R-Work) 2028
    R-Factor(R-Work) 0.1847
    R-Factor(R-Free) 0.2544
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1372
    Shell Resolution(Low) 2.1691
    Number of Reflections(R-Free) 237
    Number of Reflections(R-Work) 2132
    R-Factor(R-Work) 0.1726
    R-Factor(R-Free) 0.2284
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1691
    Shell Resolution(Low) 2.203
    Number of Reflections(R-Free) 224
    Number of Reflections(R-Work) 2013
    R-Factor(R-Work) 0.1659
    R-Factor(R-Free) 0.2328
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.203
    Shell Resolution(Low) 2.239
    Number of Reflections(R-Free) 227
    Number of Reflections(R-Work) 2045
    R-Factor(R-Work) 0.1751
    R-Factor(R-Free) 0.2566
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.239
    Shell Resolution(Low) 2.2776
    Number of Reflections(R-Free) 229
    Number of Reflections(R-Work) 2063
    R-Factor(R-Work) 0.1697
    R-Factor(R-Free) 0.2477
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2776
    Shell Resolution(Low) 2.3189
    Number of Reflections(R-Free) 226
    Number of Reflections(R-Work) 2028
    R-Factor(R-Work) 0.156
    R-Factor(R-Free) 0.2118
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3189
    Shell Resolution(Low) 2.3635
    Number of Reflections(R-Free) 227
    Number of Reflections(R-Work) 2050
    R-Factor(R-Work) 0.1493
    R-Factor(R-Free) 0.2072
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3635
    Shell Resolution(Low) 2.4116
    Number of Reflections(R-Free) 233
    Number of Reflections(R-Work) 2093
    R-Factor(R-Work) 0.1487
    R-Factor(R-Free) 0.2133
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4116
    Shell Resolution(Low) 2.464
    Number of Reflections(R-Free) 227
    Number of Reflections(R-Work) 2043
    R-Factor(R-Work) 0.1418
    R-Factor(R-Free) 0.2037
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.464
    Shell Resolution(Low) 2.5212
    Number of Reflections(R-Free) 230
    Number of Reflections(R-Work) 2069
    R-Factor(R-Work) 0.1484
    R-Factor(R-Free) 0.1951
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5212
    Shell Resolution(Low) 2.5841
    Number of Reflections(R-Free) 223
    Number of Reflections(R-Work) 2010
    R-Factor(R-Work) 0.1437
    R-Factor(R-Free) 0.2276
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5841
    Shell Resolution(Low) 2.6538
    Number of Reflections(R-Free) 236
    Number of Reflections(R-Work) 2120
    R-Factor(R-Work) 0.1483
    R-Factor(R-Free) 0.211
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6538
    Shell Resolution(Low) 2.7317
    Number of Reflections(R-Free) 225
    Number of Reflections(R-Work) 2024
    R-Factor(R-Work) 0.1442
    R-Factor(R-Free) 0.2086
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7317
    Shell Resolution(Low) 2.8197
    Number of Reflections(R-Free) 229
    Number of Reflections(R-Work) 2064
    R-Factor(R-Work) 0.1495
    R-Factor(R-Free) 0.2182
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8197
    Shell Resolution(Low) 2.9202
    Number of Reflections(R-Free) 225
    Number of Reflections(R-Work) 2022
    R-Factor(R-Work) 0.151
    R-Factor(R-Free) 0.2118
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9202
    Shell Resolution(Low) 3.0367
    Number of Reflections(R-Free) 224
    Number of Reflections(R-Work) 2014
    R-Factor(R-Work) 0.1483
    R-Factor(R-Free) 0.2056
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0367
    Shell Resolution(Low) 3.1744
    Number of Reflections(R-Free) 225
    Number of Reflections(R-Work) 2030
    R-Factor(R-Work) 0.1557
    R-Factor(R-Free) 0.2087
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1744
    Shell Resolution(Low) 3.341
    Number of Reflections(R-Free) 219
    Number of Reflections(R-Work) 1975
    R-Factor(R-Work) 0.1545
    R-Factor(R-Free) 0.1943
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.341
    Shell Resolution(Low) 3.5493
    Number of Reflections(R-Free) 213
    Number of Reflections(R-Work) 1915
    R-Factor(R-Work) 0.1473
    R-Factor(R-Free) 0.2416
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5493
    Shell Resolution(Low) 3.8215
    Number of Reflections(R-Free) 212
    Number of Reflections(R-Work) 1909
    R-Factor(R-Work) 0.1405
    R-Factor(R-Free) 0.1784
    Percent Reflections(Observed) 88.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8215
    Shell Resolution(Low) 4.2029
    Number of Reflections(R-Free) 210
    Number of Reflections(R-Work) 1884
    R-Factor(R-Work) 0.1349
    R-Factor(R-Free) 0.1655
    Percent Reflections(Observed) 88.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2029
    Shell Resolution(Low) 4.8037
    Number of Reflections(R-Free) 213
    Number of Reflections(R-Work) 1920
    R-Factor(R-Work) 0.1385
    R-Factor(R-Free) 0.1629
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8037
    Shell Resolution(Low) 6.0246
    Number of Reflections(R-Free) 223
    Number of Reflections(R-Work) 2007
    R-Factor(R-Work) 0.1909
    R-Factor(R-Free) 0.2226
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.0246
    Shell Resolution(Low) 19.9958
    Number of Reflections(R-Free) 214
    Number of Reflections(R-Work) 1927
    R-Factor(R-Work) 0.1762
    R-Factor(R-Free) 0.2229
    Percent Reflections(Observed) 90.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.005
    f_chiral_restr 0.074
    f_dihedral_angle_d 15.195
    f_angle_d 1.156
    f_bond_d 0.012
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 7044
    Nucleic Acid Atoms 0
    Heterogen Atoms 15
    Solvent Atoms 337
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XDS
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.8.1_1168)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.8.1_1168)
    model building PHASER