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X-RAY DIFFRACTION
Materials and Methods page
3QB9
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 8
    Temperature 298.0
    Details 1.8 M NaCl, 100 mM Tris-HCl (pH 8.0), 25 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 124.34 α = 90
    b = 124.34 β = 90
    c = 174.98 γ = 90
     
    Space Group
    Space Group Name:    I 4
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315r
    Collection Date 2010-12-03
     
    Diffraction Radiation
    Monochromator side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRL BEAMLINE BL7-1
    Wavelength List 1.0972109
    Site SSRL
    Beamline BL7-1
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.11
    Resolution(Low) 39.32
    Number Reflections(Observed) 75962
    Percent Possible(Observed) 99.34
    R Merge I(Observed) 0.084
    Redundancy 9.0
     
     
  •   Refinement Hide
    Refinement Statistics
    reflnsShellList 2.11
    Resolution(Low) 39.321
    Cut-off Sigma(F) 1.35
    Number of Reflections(Observed) 75688
    Number of Reflections(R-Free) 7640
    Percent Reflections(Observed) 99.27
    R-Factor(Observed) 0.1842
    R-Work 0.1783
    R-Free 0.2363
     
    Temperature Factor Modeling
    Anisotropic B[1][1] 3.373
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 3.373
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -6.7461
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1084
    Shell Resolution(Low) 2.1323
    Number of Reflections(R-Free) 229
    Number of Reflections(R-Work) 1984
    R-Factor(R-Work) 0.3655
    R-Factor(R-Free) 0.3874
    Percent Reflections(Observed) 88.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1323
    Shell Resolution(Low) 2.1574
    Number of Reflections(R-Free) 263
    Number of Reflections(R-Work) 2237
    R-Factor(R-Work) 0.3379
    R-Factor(R-Free) 0.3853
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1574
    Shell Resolution(Low) 2.1837
    Number of Reflections(R-Free) 232
    Number of Reflections(R-Work) 2282
    R-Factor(R-Work) 0.3137
    R-Factor(R-Free) 0.3452
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1837
    Shell Resolution(Low) 2.2114
    Number of Reflections(R-Free) 263
    Number of Reflections(R-Work) 2298
    R-Factor(R-Work) 0.29
    R-Factor(R-Free) 0.3096
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2114
    Shell Resolution(Low) 2.2404
    Number of Reflections(R-Free) 247
    Number of Reflections(R-Work) 2249
    R-Factor(R-Work) 0.2824
    R-Factor(R-Free) 0.3272
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2404
    Shell Resolution(Low) 2.2711
    Number of Reflections(R-Free) 247
    Number of Reflections(R-Work) 2268
    R-Factor(R-Work) 0.2888
    R-Factor(R-Free) 0.3202
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2711
    Shell Resolution(Low) 2.3036
    Number of Reflections(R-Free) 234
    Number of Reflections(R-Work) 2311
    R-Factor(R-Work) 0.2578
    R-Factor(R-Free) 0.3385
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3036
    Shell Resolution(Low) 2.338
    Number of Reflections(R-Free) 264
    Number of Reflections(R-Work) 2285
    R-Factor(R-Work) 0.2293
    R-Factor(R-Free) 0.3017
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.338
    Shell Resolution(Low) 2.3745
    Number of Reflections(R-Free) 261
    Number of Reflections(R-Work) 2241
    R-Factor(R-Work) 0.229
    R-Factor(R-Free) 0.2862
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3745
    Shell Resolution(Low) 2.4134
    Number of Reflections(R-Free) 243
    Number of Reflections(R-Work) 2271
    R-Factor(R-Work) 0.2214
    R-Factor(R-Free) 0.333
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4134
    Shell Resolution(Low) 2.455
    Number of Reflections(R-Free) 293
    Number of Reflections(R-Work) 2235
    R-Factor(R-Work) 0.2057
    R-Factor(R-Free) 0.2792
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.455
    Shell Resolution(Low) 2.4997
    Number of Reflections(R-Free) 274
    Number of Reflections(R-Work) 2248
    R-Factor(R-Work) 0.217
    R-Factor(R-Free) 0.2762
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4997
    Shell Resolution(Low) 2.5477
    Number of Reflections(R-Free) 261
    Number of Reflections(R-Work) 2295
    R-Factor(R-Work) 0.2083
    R-Factor(R-Free) 0.2808
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5477
    Shell Resolution(Low) 2.5997
    Number of Reflections(R-Free) 250
    Number of Reflections(R-Work) 2259
    R-Factor(R-Work) 0.21
    R-Factor(R-Free) 0.2843
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5997
    Shell Resolution(Low) 2.6562
    Number of Reflections(R-Free) 251
    Number of Reflections(R-Work) 2290
    R-Factor(R-Work) 0.2163
    R-Factor(R-Free) 0.2869
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6562
    Shell Resolution(Low) 2.718
    Number of Reflections(R-Free) 251
    Number of Reflections(R-Work) 2279
    R-Factor(R-Work) 0.2033
    R-Factor(R-Free) 0.2667
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.718
    Shell Resolution(Low) 2.786
    Number of Reflections(R-Free) 240
    Number of Reflections(R-Work) 2306
    R-Factor(R-Work) 0.195
    R-Factor(R-Free) 0.252
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.786
    Shell Resolution(Low) 2.8613
    Number of Reflections(R-Free) 247
    Number of Reflections(R-Work) 2286
    R-Factor(R-Work) 0.2017
    R-Factor(R-Free) 0.2706
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8613
    Shell Resolution(Low) 2.9454
    Number of Reflections(R-Free) 256
    Number of Reflections(R-Work) 2286
    R-Factor(R-Work) 0.184
    R-Factor(R-Free) 0.2586
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9454
    Shell Resolution(Low) 3.0405
    Number of Reflections(R-Free) 264
    Number of Reflections(R-Work) 2279
    R-Factor(R-Work) 0.1839
    R-Factor(R-Free) 0.2578
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0405
    Shell Resolution(Low) 3.1491
    Number of Reflections(R-Free) 241
    Number of Reflections(R-Work) 2255
    R-Factor(R-Work) 0.1711
    R-Factor(R-Free) 0.2249
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1491
    Shell Resolution(Low) 3.2751
    Number of Reflections(R-Free) 254
    Number of Reflections(R-Work) 2308
    R-Factor(R-Work) 0.1571
    R-Factor(R-Free) 0.2416
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2751
    Shell Resolution(Low) 3.4241
    Number of Reflections(R-Free) 250
    Number of Reflections(R-Work) 2272
    R-Factor(R-Work) 0.1483
    R-Factor(R-Free) 0.2368
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4241
    Shell Resolution(Low) 3.6045
    Number of Reflections(R-Free) 232
    Number of Reflections(R-Work) 2303
    R-Factor(R-Work) 0.1361
    R-Factor(R-Free) 0.1991
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6045
    Shell Resolution(Low) 3.8302
    Number of Reflections(R-Free) 242
    Number of Reflections(R-Work) 2290
    R-Factor(R-Work) 0.1316
    R-Factor(R-Free) 0.1797
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8302
    Shell Resolution(Low) 4.1256
    Number of Reflections(R-Free) 279
    Number of Reflections(R-Work) 2281
    R-Factor(R-Work) 0.1264
    R-Factor(R-Free) 0.1846
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1256
    Shell Resolution(Low) 4.5402
    Number of Reflections(R-Free) 255
    Number of Reflections(R-Work) 2275
    R-Factor(R-Work) 0.1138
    R-Factor(R-Free) 0.1598
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5402
    Shell Resolution(Low) 5.1959
    Number of Reflections(R-Free) 267
    Number of Reflections(R-Work) 2305
    R-Factor(R-Work) 0.1253
    R-Factor(R-Free) 0.1903
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1959
    Shell Resolution(Low) 6.5414
    Number of Reflections(R-Free) 266
    Number of Reflections(R-Work) 2312
    R-Factor(R-Work) 0.1705
    R-Factor(R-Free) 0.2301
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.5414
    Shell Resolution(Low) 39.3275
    Number of Reflections(R-Free) 284
    Number of Reflections(R-Work) 2258
    R-Factor(R-Work) 0.1664
    R-Factor(R-Free) 0.1944
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.004
    f_chiral_restr 0.06
    f_dihedral_angle_d 14.74
    f_angle_d 0.982
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 7710
    Nucleic Acid Atoms 0
    Heterogen Atoms 142
    Solvent Atoms 509
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Refinement PHENIX (phenix.refine: 1.7.1_743)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.6.4_486)
    data collection HKL-2000