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X-RAY DIFFRACTION
Materials and Methods page
4HD6
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion, hanging drop
    pH 6.5
    Temperature 293.0
    Details PEG 8000, sodium cacodylate, pH 6.5, vapor diffusion, hanging drop, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 48.18 α = 90
    b = 78.91 β = 106.13
    c = 85.81 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Detector
    Collection Date 2011-02-17
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID23-1
    Wavelength List 0.976300
    Site ESRF
    Beamline ID23-1
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2
    Resolution(Low) 82.43
    Number Reflections(All) 40762
    Number Reflections(Observed) 40762
    Percent Possible(Observed) 97.5
    Redundancy 2.3
     
    High Resolution Shell Details
    Resolution(High) 2.0
    Resolution(Low) 2.11
    Percent Possible(All) 96.8
    R Merge I(Observed) 0.285
    Mean I Over Sigma(Observed) 2.0
    R-Sym I(Observed) 0.285
    Redundancy 2.3
    Number Unique Reflections(All) 5892
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.0
    Resolution(Low) 41.216
    Cut-off Sigma(F) 1.33
    Number of Reflections(all) 40762
    Number of Reflections(Observed) 40605
    Number of Reflections(R-Free) 4068
    Percent Reflections(Observed) 97.15
    R-Factor(Observed) 0.248
    R-Work 0.2448
    R-Free 0.2773
     
    Temperature Factor Modeling
    Mean Isotropic B Value 25.902
    Anisotropic B[1][1] -1.3602
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 5.5002
    Anisotropic B[2][2] -5.3994
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 8.7596
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0
    Shell Resolution(Low) 2.0236
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 1242
    R-Factor(R-Work) 0.3117
    R-Factor(R-Free) 0.4036
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0236
    Shell Resolution(Low) 2.0482
    Number of Reflections(R-Free) 126
    Number of Reflections(R-Work) 1319
    R-Factor(R-Work) 0.3394
    R-Factor(R-Free) 0.3633
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0482
    Shell Resolution(Low) 2.0742
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 1199
    R-Factor(R-Work) 0.3545
    R-Factor(R-Free) 0.4049
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0742
    Shell Resolution(Low) 2.1014
    Number of Reflections(R-Free) 120
    Number of Reflections(R-Work) 1186
    R-Factor(R-Work) 0.3806
    R-Factor(R-Free) 0.4379
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1014
    Shell Resolution(Low) 2.1302
    Number of Reflections(R-Free) 117
    Number of Reflections(R-Work) 1248
    R-Factor(R-Work) 0.3212
    R-Factor(R-Free) 0.3549
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1302
    Shell Resolution(Low) 2.1607
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 1285
    R-Factor(R-Work) 0.3197
    R-Factor(R-Free) 0.3451
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1607
    Shell Resolution(Low) 2.1929
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 1311
    R-Factor(R-Work) 0.3082
    R-Factor(R-Free) 0.3318
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1929
    Shell Resolution(Low) 2.2272
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 1213
    R-Factor(R-Work) 0.314
    R-Factor(R-Free) 0.3697
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2272
    Shell Resolution(Low) 2.2637
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 1195
    R-Factor(R-Work) 0.3563
    R-Factor(R-Free) 0.3781
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2637
    Shell Resolution(Low) 2.3027
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 1228
    R-Factor(R-Work) 0.3265
    R-Factor(R-Free) 0.3838
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3027
    Shell Resolution(Low) 2.3446
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 1240
    R-Factor(R-Work) 0.2832
    R-Factor(R-Free) 0.3733
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3446
    Shell Resolution(Low) 2.3897
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 1308
    R-Factor(R-Work) 0.2632
    R-Factor(R-Free) 0.3305
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3897
    Shell Resolution(Low) 2.4384
    Number of Reflections(R-Free) 168
    Number of Reflections(R-Work) 1235
    R-Factor(R-Work) 0.2783
    R-Factor(R-Free) 0.3288
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4384
    Shell Resolution(Low) 2.4915
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 1264
    R-Factor(R-Work) 0.2596
    R-Factor(R-Free) 0.3441
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4915
    Shell Resolution(Low) 2.5494
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 1276
    R-Factor(R-Work) 0.2606
    R-Factor(R-Free) 0.2985
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5494
    Shell Resolution(Low) 2.6132
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 1256
    R-Factor(R-Work) 0.2552
    R-Factor(R-Free) 0.3012
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6132
    Shell Resolution(Low) 2.6838
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 1281
    R-Factor(R-Work) 0.2726
    R-Factor(R-Free) 0.2905
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6838
    Shell Resolution(Low) 2.7628
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 1271
    R-Factor(R-Work) 0.2689
    R-Factor(R-Free) 0.2903
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7628
    Shell Resolution(Low) 2.8519
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 1290
    R-Factor(R-Work) 0.2566
    R-Factor(R-Free) 0.2799
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8519
    Shell Resolution(Low) 2.9538
    Number of Reflections(R-Free) 158
    Number of Reflections(R-Work) 1257
    R-Factor(R-Work) 0.2398
    R-Factor(R-Free) 0.2848
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9538
    Shell Resolution(Low) 3.072
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 1265
    R-Factor(R-Work) 0.2358
    R-Factor(R-Free) 0.2579
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.072
    Shell Resolution(Low) 3.2118
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 1240
    R-Factor(R-Work) 0.2443
    R-Factor(R-Free) 0.2939
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2118
    Shell Resolution(Low) 3.3811
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 1253
    R-Factor(R-Work) 0.2362
    R-Factor(R-Free) 0.2581
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3811
    Shell Resolution(Low) 3.5928
    Number of Reflections(R-Free) 170
    Number of Reflections(R-Work) 1241
    R-Factor(R-Work) 0.2362
    R-Factor(R-Free) 0.2442
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5928
    Shell Resolution(Low) 3.87
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 1279
    R-Factor(R-Work) 0.2088
    R-Factor(R-Free) 0.2442
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.87
    Shell Resolution(Low) 4.2591
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 1280
    R-Factor(R-Work) 0.1933
    R-Factor(R-Free) 0.2101
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2591
    Shell Resolution(Low) 4.8745
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 1305
    R-Factor(R-Work) 0.1657
    R-Factor(R-Free) 0.1667
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8745
    Shell Resolution(Low) 6.1382
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 1331
    R-Factor(R-Work) 0.18
    R-Factor(R-Free) 0.1987
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.1382
    Shell Resolution(Low) 41.2248
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 1239
    R-Factor(R-Work) 0.2017
    R-Factor(R-Free) 0.2221
    Percent Reflections(Observed) 94.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 16.983
    f_plane_restr 0.008
    f_chiral_restr 0.087
    f_angle_d 1.244
    f_bond_d 0.012
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4708
    Nucleic Acid Atoms 0
    Heterogen Atoms 4
    Solvent Atoms 254
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.7.3_928)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    molecular replacement Phaser
    data reduction SCALA version: 3.3.16
    data collection Mosflm