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X-RAY DIFFRACTION
Materials and Methods page
4HNO
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 9
    Temperature 298.0
    Details 100 mM Tris-HCl pH 9.0, 4 mM DTT, 1.5% saturated MgSO4, 16% ethylene glycol, 20% mPEG2K, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 123.37 α = 90
    b = 123.37 β = 90
    c = 35.4 γ = 120
     
    Space Group
    Space Group Name:    P 61
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 90
     
    Diffraction Detector
    Detector IMAGE PLATE
    Type MAR scanner 345 mm plate
    Collection Date 1999-07-15
     
    Diffraction Radiation
    Monochromator MIRRORS POLAR 0.000
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRL BEAMLINE BL9-1
    Wavelength List 0.78
    Site SSRL
    Beamline BL9-1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 5.0
    Observed Criterion Sigma(I) 5.0
    Resolution(High) 0.92
    Resolution(Low) 30
    Number Reflections(All) 213629
    Number Reflections(Observed) 204938
    Percent Possible(Observed) 95.9
    B(Isotropic) From Wilson Plot 26.5
    Redundancy 2.84
     
    High Resolution Shell Details
    Resolution(High) 0.9194
    Resolution(Low) 0.95
    Percent Possible(All) 88.6
    R Merge I(Observed) 0.42
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 0.9194
    Resolution(Low) 24.511
    Cut-off Sigma(F) 1.34
    Number of Reflections(all) 204931
    Number of Reflections(Observed) 204917
    Number of Reflections(R-Free) 10253
    Percent Reflections(Observed) 95.92
    R-Factor(Observed) 0.1255
    R-Work 0.1248
    R-Free 0.139
     
    Temperature Factor Modeling
    Mean Isotropic B Value 17.0195
    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) 0.9194
    Shell Resolution(Low) 0.9298
    Number of Reflections(R-Free) 288
    Number of Reflections(R-Work) 5717
    R-Factor(R-Work) 0.2196
    R-Factor(R-Free) 0.2396
    Percent Reflections(Observed) 84.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 0.9298
    Shell Resolution(Low) 0.9408
    Number of Reflections(R-Free) 315
    Number of Reflections(R-Work) 6078
    R-Factor(R-Work) 0.1972
    R-Factor(R-Free) 0.2195
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 0.9408
    Shell Resolution(Low) 0.9523
    Number of Reflections(R-Free) 313
    Number of Reflections(R-Work) 6184
    R-Factor(R-Work) 0.178
    R-Factor(R-Free) 0.1881
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 0.9523
    Shell Resolution(Low) 0.9643
    Number of Reflections(R-Free) 337
    Number of Reflections(R-Work) 6337
    R-Factor(R-Work) 0.1714
    R-Factor(R-Free) 0.1783
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 0.9643
    Shell Resolution(Low) 0.977
    Number of Reflections(R-Free) 321
    Number of Reflections(R-Work) 6341
    R-Factor(R-Work) 0.161
    R-Factor(R-Free) 0.1774
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 0.977
    Shell Resolution(Low) 0.9904
    Number of Reflections(R-Free) 342
    Number of Reflections(R-Work) 6415
    R-Factor(R-Work) 0.1554
    R-Factor(R-Free) 0.1653
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 0.9904
    Shell Resolution(Low) 1.0045
    Number of Reflections(R-Free) 319
    Number of Reflections(R-Work) 6459
    R-Factor(R-Work) 0.1474
    R-Factor(R-Free) 0.1573
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.0045
    Shell Resolution(Low) 1.0195
    Number of Reflections(R-Free) 333
    Number of Reflections(R-Work) 6473
    R-Factor(R-Work) 0.1358
    R-Factor(R-Free) 0.1494
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.0195
    Shell Resolution(Low) 1.0355
    Number of Reflections(R-Free) 331
    Number of Reflections(R-Work) 6517
    R-Factor(R-Work) 0.1255
    R-Factor(R-Free) 0.1498
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.0355
    Shell Resolution(Low) 1.0524
    Number of Reflections(R-Free) 333
    Number of Reflections(R-Work) 6537
    R-Factor(R-Work) 0.1184
    R-Factor(R-Free) 0.1293
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.0524
    Shell Resolution(Low) 1.0706
    Number of Reflections(R-Free) 372
    Number of Reflections(R-Work) 6456
    R-Factor(R-Work) 0.1113
    R-Factor(R-Free) 0.1345
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.0706
    Shell Resolution(Low) 1.09
    Number of Reflections(R-Free) 347
    Number of Reflections(R-Work) 6473
    R-Factor(R-Work) 0.104
    R-Factor(R-Free) 0.1219
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.09
    Shell Resolution(Low) 1.111
    Number of Reflections(R-Free) 349
    Number of Reflections(R-Work) 6539
    R-Factor(R-Work) 0.1033
    R-Factor(R-Free) 0.1095
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.111
    Shell Resolution(Low) 1.1337
    Number of Reflections(R-Free) 362
    Number of Reflections(R-Work) 6480
    R-Factor(R-Work) 0.0981
    R-Factor(R-Free) 0.1141
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.1337
    Shell Resolution(Low) 1.1583
    Number of Reflections(R-Free) 334
    Number of Reflections(R-Work) 6497
    R-Factor(R-Work) 0.0946
    R-Factor(R-Free) 0.1148
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.1583
    Shell Resolution(Low) 1.1853
    Number of Reflections(R-Free) 372
    Number of Reflections(R-Work) 6459
    R-Factor(R-Work) 0.0974
    R-Factor(R-Free) 0.1107
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.1853
    Shell Resolution(Low) 1.2149
    Number of Reflections(R-Free) 359
    Number of Reflections(R-Work) 6470
    R-Factor(R-Work) 0.1
    R-Factor(R-Free) 0.1188
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.2149
    Shell Resolution(Low) 1.2478
    Number of Reflections(R-Free) 318
    Number of Reflections(R-Work) 6447
    R-Factor(R-Work) 0.0976
    R-Factor(R-Free) 0.1071
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.2478
    Shell Resolution(Low) 1.2845
    Number of Reflections(R-Free) 329
    Number of Reflections(R-Work) 6451
    R-Factor(R-Work) 0.1
    R-Factor(R-Free) 0.1151
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.2845
    Shell Resolution(Low) 1.3259
    Number of Reflections(R-Free) 327
    Number of Reflections(R-Work) 6434
    R-Factor(R-Work) 0.0999
    R-Factor(R-Free) 0.114
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3259
    Shell Resolution(Low) 1.3733
    Number of Reflections(R-Free) 333
    Number of Reflections(R-Work) 6606
    R-Factor(R-Work) 0.1
    R-Factor(R-Free) 0.1186
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3733
    Shell Resolution(Low) 1.4283
    Number of Reflections(R-Free) 384
    Number of Reflections(R-Work) 6719
    R-Factor(R-Work) 0.1001
    R-Factor(R-Free) 0.1159
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4283
    Shell Resolution(Low) 1.4933
    Number of Reflections(R-Free) 355
    Number of Reflections(R-Work) 6750
    R-Factor(R-Work) 0.0981
    R-Factor(R-Free) 0.1213
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4933
    Shell Resolution(Low) 1.572
    Number of Reflections(R-Free) 347
    Number of Reflections(R-Work) 6741
    R-Factor(R-Work) 0.1013
    R-Factor(R-Free) 0.111
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.572
    Shell Resolution(Low) 1.6705
    Number of Reflections(R-Free) 314
    Number of Reflections(R-Work) 6793
    R-Factor(R-Work) 0.1187
    R-Factor(R-Free) 0.1478
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6705
    Shell Resolution(Low) 1.7994
    Number of Reflections(R-Free) 366
    Number of Reflections(R-Work) 6643
    R-Factor(R-Work) 0.1243
    R-Factor(R-Free) 0.1352
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7994
    Shell Resolution(Low) 1.9805
    Number of Reflections(R-Free) 337
    Number of Reflections(R-Work) 6661
    R-Factor(R-Work) 0.122
    R-Factor(R-Free) 0.1461
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9805
    Shell Resolution(Low) 2.2669
    Number of Reflections(R-Free) 363
    Number of Reflections(R-Work) 6592
    R-Factor(R-Work) 0.1211
    R-Factor(R-Free) 0.1329
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2669
    Shell Resolution(Low) 2.8553
    Number of Reflections(R-Free) 388
    Number of Reflections(R-Work) 6778
    R-Factor(R-Work) 0.1275
    R-Factor(R-Free) 0.1436
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8553
    Shell Resolution(Low) 24.5198
    Number of Reflections(R-Free) 365
    Number of Reflections(R-Work) 6617
    R-Factor(R-Work) 0.1551
    R-Factor(R-Free) 0.1599
    Percent Reflections(Observed) 94.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.008
    f_chiral_restr 0.08
    f_dihedral_angle_d 12.775
    f_angle_d 1.311
    f_bond_d 0.017
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2267
    Nucleic Acid Atoms 0
    Heterogen Atoms 27
    Solvent Atoms 427
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution EPMR
    Structure Refinement PHENIX (phenix.refine: 1.8.1_1168)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    molecular replacement EPMR version: 2.1
    data reduction SCALEPACK