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X-RAY DIFFRACTION
Materials and Methods page
4DV0
  •   Crystallization Hide
    Crystallization Experiments
    Method HANGING DROP
    pH 6.5
    Temperature 277.0
    Details MPD, pH 6.5, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 402.11 α = 90
    b = 402.11 β = 90
    c = 174 γ = 90
     
    Space Group
    Space Group Name:    P 41 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2010-11-07
     
    Diffraction Radiation
    Monochromator Kohzu HLD8-24r
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 24-ID-C
    Wavelength List 0.98
    Site APS
    Beamline 24-ID-C
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) -3.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 3.85
    Resolution(Low) 35
    Number Reflections(All) 130659
    Number Reflections(Observed) 130659
    Percent Possible(Observed) 97.6
    R Merge I(Observed) 0.071
    Redundancy 3.2
     
    High Resolution Shell Details
    Resolution(High) 3.85
    Resolution(Low) 3.99
    Percent Possible(All) 99.5
    R Merge I(Observed) 0.817
    Redundancy 3.2
    Number Unique Reflections(All) 13123
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 3.853
    Resolution(Low) 34.823
    Cut-off Sigma(F) 1.34
    Number of Reflections(all) 130643
    Number of Reflections(Observed) 130643
    Number of Reflections(R-Free) 6509
    Percent Reflections(Observed) 97.65
    R-Factor(Observed) 0.1504
    R-Work 0.1475
    R-Free 0.2059
    R-Free Selection Details FROM PDB ENTRY 2VQE
     
    Temperature Factor Modeling
    Mean Isotropic B Value 196.63
    Anisotropic B[1][1] -10.2483
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -10.2483
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 10.0849
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.853
    Shell Resolution(Low) 3.8969
    Number of Reflections(R-Free) 229
    Number of Reflections(R-Work) 4098
    R-Factor(R-Work) 0.2729
    R-Factor(R-Free) 0.299
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8969
    Shell Resolution(Low) 3.9426
    Number of Reflections(R-Free) 209
    Number of Reflections(R-Work) 4191
    R-Factor(R-Work) 0.2539
    R-Factor(R-Free) 0.329
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9426
    Shell Resolution(Low) 3.9906
    Number of Reflections(R-Free) 212
    Number of Reflections(R-Work) 4137
    R-Factor(R-Work) 0.2504
    R-Factor(R-Free) 0.3011
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9906
    Shell Resolution(Low) 4.0411
    Number of Reflections(R-Free) 237
    Number of Reflections(R-Work) 4177
    R-Factor(R-Work) 0.2441
    R-Factor(R-Free) 0.3193
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0411
    Shell Resolution(Low) 4.0942
    Number of Reflections(R-Free) 247
    Number of Reflections(R-Work) 4147
    R-Factor(R-Work) 0.2376
    R-Factor(R-Free) 0.3073
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0942
    Shell Resolution(Low) 4.1502
    Number of Reflections(R-Free) 208
    Number of Reflections(R-Work) 4164
    R-Factor(R-Work) 0.215
    R-Factor(R-Free) 0.2857
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1502
    Shell Resolution(Low) 4.2094
    Number of Reflections(R-Free) 225
    Number of Reflections(R-Work) 4169
    R-Factor(R-Work) 0.2013
    R-Factor(R-Free) 0.2971
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2094
    Shell Resolution(Low) 4.2721
    Number of Reflections(R-Free) 191
    Number of Reflections(R-Work) 4164
    R-Factor(R-Work) 0.197
    R-Factor(R-Free) 0.257
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2721
    Shell Resolution(Low) 4.3387
    Number of Reflections(R-Free) 249
    Number of Reflections(R-Work) 4179
    R-Factor(R-Work) 0.1873
    R-Factor(R-Free) 0.256
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3387
    Shell Resolution(Low) 4.4097
    Number of Reflections(R-Free) 219
    Number of Reflections(R-Work) 4150
    R-Factor(R-Work) 0.1796
    R-Factor(R-Free) 0.2305
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4097
    Shell Resolution(Low) 4.4856
    Number of Reflections(R-Free) 248
    Number of Reflections(R-Work) 4126
    R-Factor(R-Work) 0.1591
    R-Factor(R-Free) 0.2116
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4856
    Shell Resolution(Low) 4.567
    Number of Reflections(R-Free) 218
    Number of Reflections(R-Work) 4209
    R-Factor(R-Work) 0.1522
    R-Factor(R-Free) 0.1922
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.567
    Shell Resolution(Low) 4.6546
    Number of Reflections(R-Free) 203
    Number of Reflections(R-Work) 4149
    R-Factor(R-Work) 0.1414
    R-Factor(R-Free) 0.1884
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6546
    Shell Resolution(Low) 4.7494
    Number of Reflections(R-Free) 198
    Number of Reflections(R-Work) 4181
    R-Factor(R-Work) 0.137
    R-Factor(R-Free) 0.2163
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7494
    Shell Resolution(Low) 4.8524
    Number of Reflections(R-Free) 208
    Number of Reflections(R-Work) 4174
    R-Factor(R-Work) 0.1332
    R-Factor(R-Free) 0.1909
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8524
    Shell Resolution(Low) 4.965
    Number of Reflections(R-Free) 233
    Number of Reflections(R-Work) 4150
    R-Factor(R-Work) 0.1184
    R-Factor(R-Free) 0.1703
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.965
    Shell Resolution(Low) 5.0888
    Number of Reflections(R-Free) 215
    Number of Reflections(R-Work) 4173
    R-Factor(R-Work) 0.1153
    R-Factor(R-Free) 0.1759
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0888
    Shell Resolution(Low) 5.226
    Number of Reflections(R-Free) 199
    Number of Reflections(R-Work) 4139
    R-Factor(R-Work) 0.1084
    R-Factor(R-Free) 0.179
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.226
    Shell Resolution(Low) 5.3792
    Number of Reflections(R-Free) 214
    Number of Reflections(R-Work) 4160
    R-Factor(R-Work) 0.1091
    R-Factor(R-Free) 0.1764
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.3792
    Shell Resolution(Low) 5.5522
    Number of Reflections(R-Free) 223
    Number of Reflections(R-Work) 4167
    R-Factor(R-Work) 0.1078
    R-Factor(R-Free) 0.1678
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.5522
    Shell Resolution(Low) 5.7497
    Number of Reflections(R-Free) 221
    Number of Reflections(R-Work) 4113
    R-Factor(R-Work) 0.1105
    R-Factor(R-Free) 0.1869
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.7497
    Shell Resolution(Low) 5.9789
    Number of Reflections(R-Free) 196
    Number of Reflections(R-Work) 4165
    R-Factor(R-Work) 0.1144
    R-Factor(R-Free) 0.1712
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.9789
    Shell Resolution(Low) 6.2495
    Number of Reflections(R-Free) 202
    Number of Reflections(R-Work) 4129
    R-Factor(R-Work) 0.1186
    R-Factor(R-Free) 0.1902
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.2495
    Shell Resolution(Low) 6.5769
    Number of Reflections(R-Free) 212
    Number of Reflections(R-Work) 4131
    R-Factor(R-Work) 0.1144
    R-Factor(R-Free) 0.1669
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.5769
    Shell Resolution(Low) 6.9859
    Number of Reflections(R-Free) 205
    Number of Reflections(R-Work) 4138
    R-Factor(R-Work) 0.1076
    R-Factor(R-Free) 0.1877
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.9859
    Shell Resolution(Low) 7.5202
    Number of Reflections(R-Free) 235
    Number of Reflections(R-Work) 4091
    R-Factor(R-Work) 0.11
    R-Factor(R-Free) 0.1777
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.5202
    Shell Resolution(Low) 8.2678
    Number of Reflections(R-Free) 193
    Number of Reflections(R-Work) 4140
    R-Factor(R-Work) 0.117
    R-Factor(R-Free) 0.181
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.2678
    Shell Resolution(Low) 9.4433
    Number of Reflections(R-Free) 241
    Number of Reflections(R-Work) 4051
    R-Factor(R-Work) 0.1246
    R-Factor(R-Free) 0.183
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 9.4433
    Shell Resolution(Low) 11.8198
    Number of Reflections(R-Free) 213
    Number of Reflections(R-Work) 4139
    R-Factor(R-Work) 0.1332
    R-Factor(R-Free) 0.1886
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 11.8198
    Shell Resolution(Low) 34.824
    Number of Reflections(R-Free) 206
    Number of Reflections(R-Work) 3833
    R-Factor(R-Work) 0.2101
    R-Factor(R-Free) 0.2365
    Percent Reflections(Observed) 85.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 19.524
    f_plane_restr 0.008
    f_chiral_restr 0.082
    f_angle_d 1.428
    f_bond_d 0.011
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 19088
    Nucleic Acid Atoms 32510
    Heterogen Atoms 279
    Solvent Atoms 439
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution PHENIX (phenix.refine: dev_978)
    Structure Refinement PHENIX (phenix.refine: dev_978)
     
    Software
    data extraction pdb_extract version: 3.10
    refinement phenix
    data reduction SCALEPACK
    data collection DENZO