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X-RAY DIFFRACTION
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4DV1
  •   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 = 403.45 α = 90
    b = 403.45 β = 90
    c = 173.41 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 HLD8-24
    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) 131031
    Number Reflections(Observed) 131031
    Percent Possible(Observed) 97.3
    R Merge I(Observed) 0.075
    Redundancy 3.0
     
    High Resolution Shell Details
    Resolution(High) 3.849
    Resolution(Low) 3.99
    Percent Possible(All) 99.0
    R Merge I(Observed) 0.724
    Redundancy 3.0
    Number Unique Reflections(All) 13130
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 3.849
    Resolution(Low) 34.93
    Cut-off Sigma(F) 1.33
    Number of Reflections(all) 130989
    Number of Reflections(Observed) 130989
    Number of Reflections(R-Free) 6511
    Percent Reflections(Observed) 97.29
    R-Factor(Observed) 0.1531
    R-Work 0.1501
    R-Free 0.2116
    R-Free Selection Details FROM PDB ENTRY 2VQE
     
    Temperature Factor Modeling
    Mean Isotropic B Value 198.966
    Anisotropic B[1][1] -13.4379
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -13.4379
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 16.5628
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.849
    Shell Resolution(Low) 3.8928
    Number of Reflections(R-Free) 215
    Number of Reflections(R-Work) 4119
    R-Factor(R-Work) 0.2681
    R-Factor(R-Free) 0.3079
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8928
    Shell Resolution(Low) 3.9386
    Number of Reflections(R-Free) 214
    Number of Reflections(R-Work) 4184
    R-Factor(R-Work) 0.2688
    R-Factor(R-Free) 0.3179
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9386
    Shell Resolution(Low) 3.9865
    Number of Reflections(R-Free) 215
    Number of Reflections(R-Work) 4148
    R-Factor(R-Work) 0.2587
    R-Factor(R-Free) 0.3483
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9865
    Shell Resolution(Low) 4.0369
    Number of Reflections(R-Free) 239
    Number of Reflections(R-Work) 4177
    R-Factor(R-Work) 0.2476
    R-Factor(R-Free) 0.3271
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0369
    Shell Resolution(Low) 4.09
    Number of Reflections(R-Free) 237
    Number of Reflections(R-Work) 4111
    R-Factor(R-Work) 0.2334
    R-Factor(R-Free) 0.3023
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.09
    Shell Resolution(Low) 4.1459
    Number of Reflections(R-Free) 225
    Number of Reflections(R-Work) 4168
    R-Factor(R-Work) 0.2215
    R-Factor(R-Free) 0.2897
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1459
    Shell Resolution(Low) 4.205
    Number of Reflections(R-Free) 215
    Number of Reflections(R-Work) 4147
    R-Factor(R-Work) 0.2073
    R-Factor(R-Free) 0.2854
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.205
    Shell Resolution(Low) 4.2677
    Number of Reflections(R-Free) 180
    Number of Reflections(R-Work) 4220
    R-Factor(R-Work) 0.1904
    R-Factor(R-Free) 0.2658
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2677
    Shell Resolution(Low) 4.3343
    Number of Reflections(R-Free) 247
    Number of Reflections(R-Work) 4170
    R-Factor(R-Work) 0.1831
    R-Factor(R-Free) 0.2539
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3343
    Shell Resolution(Low) 4.4052
    Number of Reflections(R-Free) 221
    Number of Reflections(R-Work) 4121
    R-Factor(R-Work) 0.1676
    R-Factor(R-Free) 0.2172
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4052
    Shell Resolution(Low) 4.481
    Number of Reflections(R-Free) 247
    Number of Reflections(R-Work) 4156
    R-Factor(R-Work) 0.165
    R-Factor(R-Free) 0.2427
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.481
    Shell Resolution(Low) 4.5623
    Number of Reflections(R-Free) 220
    Number of Reflections(R-Work) 4146
    R-Factor(R-Work) 0.1674
    R-Factor(R-Free) 0.2083
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5623
    Shell Resolution(Low) 4.6499
    Number of Reflections(R-Free) 212
    Number of Reflections(R-Work) 4149
    R-Factor(R-Work) 0.1535
    R-Factor(R-Free) 0.2215
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6499
    Shell Resolution(Low) 4.7445
    Number of Reflections(R-Free) 191
    Number of Reflections(R-Work) 4170
    R-Factor(R-Work) 0.1518
    R-Factor(R-Free) 0.2154
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7445
    Shell Resolution(Low) 4.8474
    Number of Reflections(R-Free) 207
    Number of Reflections(R-Work) 4197
    R-Factor(R-Work) 0.1419
    R-Factor(R-Free) 0.2298
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8474
    Shell Resolution(Low) 4.9599
    Number of Reflections(R-Free) 233
    Number of Reflections(R-Work) 4151
    R-Factor(R-Work) 0.1308
    R-Factor(R-Free) 0.1833
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9599
    Shell Resolution(Low) 5.0836
    Number of Reflections(R-Free) 221
    Number of Reflections(R-Work) 4150
    R-Factor(R-Work) 0.1256
    R-Factor(R-Free) 0.1905
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0836
    Shell Resolution(Low) 5.2206
    Number of Reflections(R-Free) 195
    Number of Reflections(R-Work) 4191
    R-Factor(R-Work) 0.1208
    R-Factor(R-Free) 0.1906
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2206
    Shell Resolution(Low) 5.3737
    Number of Reflections(R-Free) 208
    Number of Reflections(R-Work) 4156
    R-Factor(R-Work) 0.1168
    R-Factor(R-Free) 0.1795
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.3737
    Shell Resolution(Low) 5.5465
    Number of Reflections(R-Free) 224
    Number of Reflections(R-Work) 4140
    R-Factor(R-Work) 0.1148
    R-Factor(R-Free) 0.1733
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.5465
    Shell Resolution(Low) 5.7439
    Number of Reflections(R-Free) 217
    Number of Reflections(R-Work) 4162
    R-Factor(R-Work) 0.1156
    R-Factor(R-Free) 0.2009
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.7439
    Shell Resolution(Low) 5.9728
    Number of Reflections(R-Free) 205
    Number of Reflections(R-Work) 4189
    R-Factor(R-Work) 0.1163
    R-Factor(R-Free) 0.1769
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.9728
    Shell Resolution(Low) 6.2431
    Number of Reflections(R-Free) 205
    Number of Reflections(R-Work) 4151
    R-Factor(R-Work) 0.118
    R-Factor(R-Free) 0.1852
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.2431
    Shell Resolution(Low) 6.5702
    Number of Reflections(R-Free) 206
    Number of Reflections(R-Work) 4180
    R-Factor(R-Work) 0.1209
    R-Factor(R-Free) 0.1791
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.5702
    Shell Resolution(Low) 6.9788
    Number of Reflections(R-Free) 212
    Number of Reflections(R-Work) 4155
    R-Factor(R-Work) 0.114
    R-Factor(R-Free) 0.19
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.9788
    Shell Resolution(Low) 7.5127
    Number of Reflections(R-Free) 236
    Number of Reflections(R-Work) 4138
    R-Factor(R-Work) 0.1149
    R-Factor(R-Free) 0.1824
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.5127
    Shell Resolution(Low) 8.2597
    Number of Reflections(R-Free) 195
    Number of Reflections(R-Work) 4172
    R-Factor(R-Work) 0.1179
    R-Factor(R-Free) 0.1864
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.2597
    Shell Resolution(Low) 9.4342
    Number of Reflections(R-Free) 237
    Number of Reflections(R-Work) 4031
    R-Factor(R-Work) 0.1209
    R-Factor(R-Free) 0.1709
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 9.4342
    Shell Resolution(Low) 11.8093
    Number of Reflections(R-Free) 213
    Number of Reflections(R-Work) 4163
    R-Factor(R-Work) 0.1245
    R-Factor(R-Free) 0.1755
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 11.8093
    Shell Resolution(Low) 34.9312
    Number of Reflections(R-Free) 219
    Number of Reflections(R-Work) 3966
    R-Factor(R-Work) 0.2067
    R-Factor(R-Free) 0.2511
    Percent Reflections(Observed) 87.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 19.867
    f_plane_restr 0.009
    f_chiral_restr 0.086
    f_angle_d 1.52
    f_bond_d 0.012
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 19088
    Nucleic Acid Atoms 32510
    Heterogen Atoms 289
    Solvent Atoms 410
     
     
  •   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