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X-RAY DIFFRACTION
Materials and Methods page
4DQ7
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion, hanging drop
    pH 6.5
    Temperature 289.0
    Details 1.6 M Na-Acetate, 0.1 M Na-Citrate, pH 6.5, vapor diffusion, hanging drop, temperature 289K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 62.12 α = 90
    b = 68.72 β = 90
    c = 89.89 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Collection Date 2011-01-01
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X29A
    Wavelength List 1.075
    Site NSLS
    Beamline X29A
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 1.4
    Resolution(Low) 50
    Number Reflections(All) 77799
    Number Reflections(Observed) 73877
    Percent Possible(Observed) 96.5
    R Merge I(Observed) 0.052
    Redundancy 4.3
     
    High Resolution Shell Details
    Resolution(High) 1.4
    Resolution(Low) 1.42
    Percent Possible(All) 94.5
    Redundancy 4.1
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.4
    Resolution(Low) 41.01
    Cut-off Sigma(F) 1.34
    Number of Reflections(Observed) 73824
    Number of Reflections(R-Free) 7379
    Percent Reflections(Observed) 96.3
    R-Factor(Observed) 0.178
    R-Work 0.175
    R-Free 0.198
     
    Temperature Factor Modeling
    Mean Isotropic B Value 31.13
    Anisotropic B[1][1] 0.0
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.0
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.0
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4
    Shell Resolution(Low) 1.4143
    Number of Reflections(R-Free) 218
    Number of Reflections(R-Work) 1986
    R-Factor(R-Work) 0.3712
    R-Factor(R-Free) 0.3757
    Percent Reflections(Observed) 87.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4143
    Shell Resolution(Low) 1.431
    Number of Reflections(R-Free) 234
    Number of Reflections(R-Work) 2145
    R-Factor(R-Work) 0.3599
    R-Factor(R-Free) 0.3865
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.431
    Shell Resolution(Low) 1.4484
    Number of Reflections(R-Free) 242
    Number of Reflections(R-Work) 2160
    R-Factor(R-Work) 0.3285
    R-Factor(R-Free) 0.3097
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4484
    Shell Resolution(Low) 1.4668
    Number of Reflections(R-Free) 239
    Number of Reflections(R-Work) 2136
    R-Factor(R-Work) 0.2976
    R-Factor(R-Free) 0.3412
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4668
    Shell Resolution(Low) 1.4861
    Number of Reflections(R-Free) 241
    Number of Reflections(R-Work) 2143
    R-Factor(R-Work) 0.2743
    R-Factor(R-Free) 0.2794
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4861
    Shell Resolution(Low) 1.5064
    Number of Reflections(R-Free) 242
    Number of Reflections(R-Work) 2147
    R-Factor(R-Work) 0.2555
    R-Factor(R-Free) 0.2315
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5064
    Shell Resolution(Low) 1.5279
    Number of Reflections(R-Free) 241
    Number of Reflections(R-Work) 2193
    R-Factor(R-Work) 0.2427
    R-Factor(R-Free) 0.2357
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5279
    Shell Resolution(Low) 1.5507
    Number of Reflections(R-Free) 229
    Number of Reflections(R-Work) 2171
    R-Factor(R-Work) 0.2193
    R-Factor(R-Free) 0.2737
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5507
    Shell Resolution(Low) 1.575
    Number of Reflections(R-Free) 249
    Number of Reflections(R-Work) 2167
    R-Factor(R-Work) 0.2185
    R-Factor(R-Free) 0.1871
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.575
    Shell Resolution(Low) 1.6008
    Number of Reflections(R-Free) 247
    Number of Reflections(R-Work) 2185
    R-Factor(R-Work) 0.2081
    R-Factor(R-Free) 0.243
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6008
    Shell Resolution(Low) 1.6284
    Number of Reflections(R-Free) 237
    Number of Reflections(R-Work) 2191
    R-Factor(R-Work) 0.1895
    R-Factor(R-Free) 0.2333
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6284
    Shell Resolution(Low) 1.658
    Number of Reflections(R-Free) 247
    Number of Reflections(R-Work) 2191
    R-Factor(R-Work) 0.1796
    R-Factor(R-Free) 0.1925
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.658
    Shell Resolution(Low) 1.6899
    Number of Reflections(R-Free) 243
    Number of Reflections(R-Work) 2192
    R-Factor(R-Work) 0.176
    R-Factor(R-Free) 0.1903
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6899
    Shell Resolution(Low) 1.7244
    Number of Reflections(R-Free) 245
    Number of Reflections(R-Work) 2199
    R-Factor(R-Work) 0.1769
    R-Factor(R-Free) 0.1963
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7244
    Shell Resolution(Low) 1.7619
    Number of Reflections(R-Free) 247
    Number of Reflections(R-Work) 2229
    R-Factor(R-Work) 0.1733
    R-Factor(R-Free) 0.2115
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7619
    Shell Resolution(Low) 1.8029
    Number of Reflections(R-Free) 246
    Number of Reflections(R-Work) 2180
    R-Factor(R-Work) 0.175
    R-Factor(R-Free) 0.204
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8029
    Shell Resolution(Low) 1.848
    Number of Reflections(R-Free) 253
    Number of Reflections(R-Work) 2257
    R-Factor(R-Work) 0.1734
    R-Factor(R-Free) 0.1937
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.848
    Shell Resolution(Low) 1.8979
    Number of Reflections(R-Free) 245
    Number of Reflections(R-Work) 2200
    R-Factor(R-Work) 0.1671
    R-Factor(R-Free) 0.1808
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8979
    Shell Resolution(Low) 1.9538
    Number of Reflections(R-Free) 252
    Number of Reflections(R-Work) 2252
    R-Factor(R-Work) 0.1665
    R-Factor(R-Free) 0.1788
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9538
    Shell Resolution(Low) 2.0168
    Number of Reflections(R-Free) 250
    Number of Reflections(R-Work) 2233
    R-Factor(R-Work) 0.1669
    R-Factor(R-Free) 0.181
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0168
    Shell Resolution(Low) 2.0889
    Number of Reflections(R-Free) 246
    Number of Reflections(R-Work) 2246
    R-Factor(R-Work) 0.1606
    R-Factor(R-Free) 0.1728
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0889
    Shell Resolution(Low) 2.1726
    Number of Reflections(R-Free) 247
    Number of Reflections(R-Work) 2240
    R-Factor(R-Work) 0.1614
    R-Factor(R-Free) 0.1915
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1726
    Shell Resolution(Low) 2.2714
    Number of Reflections(R-Free) 252
    Number of Reflections(R-Work) 2283
    R-Factor(R-Work) 0.1529
    R-Factor(R-Free) 0.1711
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2714
    Shell Resolution(Low) 2.3912
    Number of Reflections(R-Free) 251
    Number of Reflections(R-Work) 2266
    R-Factor(R-Work) 0.1484
    R-Factor(R-Free) 0.1652
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3912
    Shell Resolution(Low) 2.541
    Number of Reflections(R-Free) 253
    Number of Reflections(R-Work) 2286
    R-Factor(R-Work) 0.1569
    R-Factor(R-Free) 0.178
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.541
    Shell Resolution(Low) 2.7371
    Number of Reflections(R-Free) 251
    Number of Reflections(R-Work) 2299
    R-Factor(R-Work) 0.1626
    R-Factor(R-Free) 0.2032
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7371
    Shell Resolution(Low) 3.0125
    Number of Reflections(R-Free) 257
    Number of Reflections(R-Work) 2297
    R-Factor(R-Work) 0.1787
    R-Factor(R-Free) 0.1983
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0125
    Shell Resolution(Low) 3.4482
    Number of Reflections(R-Free) 258
    Number of Reflections(R-Work) 2325
    R-Factor(R-Work) 0.1675
    R-Factor(R-Free) 0.1861
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4482
    Shell Resolution(Low) 4.3436
    Number of Reflections(R-Free) 256
    Number of Reflections(R-Work) 2305
    R-Factor(R-Work) 0.1536
    R-Factor(R-Free) 0.1675
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3436
    Shell Resolution(Low) 41.0262
    Number of Reflections(R-Free) 261
    Number of Reflections(R-Work) 2341
    R-Factor(R-Work) 0.1936
    R-Factor(R-Free) 0.2359
    Percent Reflections(Observed) 94.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.004
    f_chiral_restr 0.131
    f_dihedral_angle_d 14.639
    f_angle_d 1.001
    f_bond_d 0.005
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2577
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 339
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (data scaling) SCALEPACK
    Structure Refinement PHENIX (PHENIX.REFINE: 1.7.3_928)
     
    Software
    data extraction pdb_extract version: 3.10
    refinement phenix
    data reduction SCALEPACK