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X-RAY DIFFRACTION
Materials and Methods page
3KSB
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.5
    Temperature 295.0
    Details 4-5% isopropanol, optimised mixture of salts, 50mM Na cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 116.76 α = 90
    b = 116.76 β = 90
    c = 182.81 γ = 120
     
    Space Group
    Space Group Name:    P 32
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2009-08-07
     
    Diffraction Radiation
    Monochromator Double crystal
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type DIAMOND BEAMLINE I03
    Wavelength List 0.9763
    Site DIAMOND
    Beamline I03
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) -3.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 3.5
    Resolution(Low) 50
    Number Reflections(Observed) 34407
    Percent Possible(Observed) 97.7
    R Merge I(Observed) 0.065
    B(Isotropic) From Wilson Plot 134.28
    Redundancy 6.1
     
    High Resolution Shell Details
    Resolution(High) 3.5
    Resolution(Low) 3.63
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.4
    Mean I Over Sigma(Observed) 4.325
    R-Sym I(Observed) 0.4
    Redundancy 6.5
    Number Unique Reflections(All) 3529
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 3.5
    Resolution(Low) 29.318
    Cut-off Sigma(F) 1.97
    Number of Reflections(Observed) 34220
    Number of Reflections(R-Free) 3524
    Percent Reflections(Observed) 97.53
    R-Factor(Observed) 0.1859
    R-Work 0.1813
    R-Free 0.2257
    R-Free Selection Details random
     
    Temperature Factor Modeling
    Isotropic Thermal Model Isotropic+TLS
    Mean Isotropic B Value 147.717
    Anisotropic B[1][1] -4.813
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -4.813
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -25.078
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5001
    Shell Resolution(Low) 3.5479
    Number of Reflections(R-Free) 158
    Number of Reflections(R-Work) 1269
    R-Factor(R-Work) 0.2629
    R-Factor(R-Free) 0.3279
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5479
    Shell Resolution(Low) 3.5985
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 1215
    R-Factor(R-Work) 0.2561
    R-Factor(R-Free) 0.2713
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5985
    Shell Resolution(Low) 3.6521
    Number of Reflections(R-Free) 124
    Number of Reflections(R-Work) 1268
    R-Factor(R-Work) 0.225
    R-Factor(R-Free) 0.3055
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6521
    Shell Resolution(Low) 3.7091
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 1250
    R-Factor(R-Work) 0.2207
    R-Factor(R-Free) 0.2481
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7091
    Shell Resolution(Low) 3.7698
    Number of Reflections(R-Free) 162
    Number of Reflections(R-Work) 1281
    R-Factor(R-Work) 0.1961
    R-Factor(R-Free) 0.2635
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7698
    Shell Resolution(Low) 3.8347
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 1207
    R-Factor(R-Work) 0.1924
    R-Factor(R-Free) 0.2465
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8347
    Shell Resolution(Low) 3.9042
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 1275
    R-Factor(R-Work) 0.1704
    R-Factor(R-Free) 0.1982
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9042
    Shell Resolution(Low) 3.9792
    Number of Reflections(R-Free) 123
    Number of Reflections(R-Work) 1257
    R-Factor(R-Work) 0.1646
    R-Factor(R-Free) 0.2185
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9792
    Shell Resolution(Low) 4.0602
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 1267
    R-Factor(R-Work) 0.1656
    R-Factor(R-Free) 0.2634
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0602
    Shell Resolution(Low) 4.1482
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 1233
    R-Factor(R-Work) 0.1602
    R-Factor(R-Free) 0.2213
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1482
    Shell Resolution(Low) 4.2444
    Number of Reflections(R-Free) 156
    Number of Reflections(R-Work) 1245
    R-Factor(R-Work) 0.1552
    R-Factor(R-Free) 0.203
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2444
    Shell Resolution(Low) 4.3503
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 1273
    R-Factor(R-Work) 0.1369
    R-Factor(R-Free) 0.2077
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3503
    Shell Resolution(Low) 4.4675
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 1245
    R-Factor(R-Work) 0.1238
    R-Factor(R-Free) 0.1661
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4675
    Shell Resolution(Low) 4.5985
    Number of Reflections(R-Free) 169
    Number of Reflections(R-Work) 1236
    R-Factor(R-Work) 0.1168
    R-Factor(R-Free) 0.1515
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5985
    Shell Resolution(Low) 4.7463
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 1235
    R-Factor(R-Work) 0.1242
    R-Factor(R-Free) 0.1757
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7463
    Shell Resolution(Low) 4.9152
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 1301
    R-Factor(R-Work) 0.1329
    R-Factor(R-Free) 0.1957
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9152
    Shell Resolution(Low) 5.111
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 1248
    R-Factor(R-Work) 0.1449
    R-Factor(R-Free) 0.2051
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.111
    Shell Resolution(Low) 5.3423
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 1259
    R-Factor(R-Work) 0.157
    R-Factor(R-Free) 0.2065
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.3423
    Shell Resolution(Low) 5.622
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 1276
    R-Factor(R-Work) 0.1695
    R-Factor(R-Free) 0.2402
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.622
    Shell Resolution(Low) 5.9715
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 1233
    R-Factor(R-Work) 0.1926
    R-Factor(R-Free) 0.2327
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.9715
    Shell Resolution(Low) 6.4281
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 1280
    R-Factor(R-Work) 0.1852
    R-Factor(R-Free) 0.2655
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.4281
    Shell Resolution(Low) 7.0668
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 1257
    R-Factor(R-Work) 0.1812
    R-Factor(R-Free) 0.25
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.0668
    Shell Resolution(Low) 8.0706
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 1270
    R-Factor(R-Work) 0.1766
    R-Factor(R-Free) 0.2066
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.0706
    Shell Resolution(Low) 10.0986
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 1142
    R-Factor(R-Work) 0.1816
    R-Factor(R-Free) 0.1722
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 10.0986
    Shell Resolution(Low) 29.319
    Number of Reflections(R-Free) 83
    Number of Reflections(R-Work) 674
    R-Factor(R-Work) 0.2492
    R-Factor(R-Free) 0.2467
    Percent Reflections(Observed) 54.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 20.065
    f_plane_restr 0.006
    f_chiral_restr 0.095
    f_angle_d 1.441
    f_bond_d 0.027
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 9865
    Nucleic Acid Atoms 730
    Heterogen Atoms 2
    Solvent Atoms 4
     
     
  •   Software and Computing Hide
    Computing
    Data Collection GDA
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution Phaser
    Structure Refinement PHENIX (phenix.refine)
     
    Software
    refinement PHENIX version: (phenix.refine)
    model building Phaser
    data collection GDA