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X-RAY DIFFRACTION
Materials and Methods page
3KSA
  •   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 = 116.91 α = 90
    b = 116.91 β = 90
    c = 183.76 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) 3.3
    Resolution(Low) 50
    Number Reflections(Observed) 41533
    Percent Possible(Observed) 98.0
    R Merge I(Observed) 0.08
    B(Isotropic) From Wilson Plot 116.06
    Redundancy 5.7
     
    High Resolution Shell Details
    Resolution(High) 3.3
    Resolution(Low) 3.42
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.461
    Mean I Over Sigma(Observed) 3.512
    R-Sym I(Observed) 0.461
    Redundancy 5.7
    Number Unique Reflections(All) 4232
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 3.3
    Resolution(Low) 29.403
    Cut-off Sigma(F) 1.96
    Number of Reflections(Observed) 41250
    Number of Reflections(R-Free) 4164
    Percent Reflections(Observed) 97.77
    R-Factor(Observed) 0.1805
    R-Work 0.1762
    R-Free 0.2181
    R-Free Selection Details random
     
    Temperature Factor Modeling
    Isotropic Thermal Model Isotropic+TLS
    Mean Isotropic B Value 136.591
    Anisotropic B[1][1] 1.332
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 1.332
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -49.123
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3
    Shell Resolution(Low) 3.3375
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 1268
    R-Factor(R-Work) 0.2966
    R-Factor(R-Free) 0.3576
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3375
    Shell Resolution(Low) 3.3767
    Number of Reflections(R-Free) 108
    Number of Reflections(R-Work) 1248
    R-Factor(R-Work) 0.2589
    R-Factor(R-Free) 0.3095
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3767
    Shell Resolution(Low) 3.4178
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 1313
    R-Factor(R-Work) 0.2633
    R-Factor(R-Free) 0.3319
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4178
    Shell Resolution(Low) 3.461
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 1248
    R-Factor(R-Work) 0.2608
    R-Factor(R-Free) 0.3515
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.461
    Shell Resolution(Low) 3.5065
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 1286
    R-Factor(R-Work) 0.2354
    R-Factor(R-Free) 0.3219
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5065
    Shell Resolution(Low) 3.5545
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 1241
    R-Factor(R-Work) 0.2194
    R-Factor(R-Free) 0.2726
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5545
    Shell Resolution(Low) 3.6051
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 1238
    R-Factor(R-Work) 0.2206
    R-Factor(R-Free) 0.2348
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6051
    Shell Resolution(Low) 3.6589
    Number of Reflections(R-Free) 124
    Number of Reflections(R-Work) 1284
    R-Factor(R-Work) 0.2126
    R-Factor(R-Free) 0.2735
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6589
    Shell Resolution(Low) 3.7159
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 1247
    R-Factor(R-Work) 0.1984
    R-Factor(R-Free) 0.2384
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7159
    Shell Resolution(Low) 3.7767
    Number of Reflections(R-Free) 160
    Number of Reflections(R-Work) 1265
    R-Factor(R-Work) 0.1754
    R-Factor(R-Free) 0.2302
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7767
    Shell Resolution(Low) 3.8417
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 1225
    R-Factor(R-Work) 0.1803
    R-Factor(R-Free) 0.2377
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8417
    Shell Resolution(Low) 3.9114
    Number of Reflections(R-Free) 161
    Number of Reflections(R-Work) 1289
    R-Factor(R-Work) 0.1647
    R-Factor(R-Free) 0.2005
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9114
    Shell Resolution(Low) 3.9865
    Number of Reflections(R-Free) 114
    Number of Reflections(R-Work) 1216
    R-Factor(R-Work) 0.1612
    R-Factor(R-Free) 0.1994
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9865
    Shell Resolution(Low) 4.0676
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 1263
    R-Factor(R-Work) 0.1614
    R-Factor(R-Free) 0.233
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0676
    Shell Resolution(Low) 4.1558
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 1275
    R-Factor(R-Work) 0.1553
    R-Factor(R-Free) 0.2202
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1558
    Shell Resolution(Low) 4.2522
    Number of Reflections(R-Free) 158
    Number of Reflections(R-Work) 1244
    R-Factor(R-Work) 0.1571
    R-Factor(R-Free) 0.209
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2522
    Shell Resolution(Low) 4.3583
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 1261
    R-Factor(R-Work) 0.1329
    R-Factor(R-Free) 0.1937
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3583
    Shell Resolution(Low) 4.4757
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 1262
    R-Factor(R-Work) 0.122
    R-Factor(R-Free) 0.1741
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4757
    Shell Resolution(Low) 4.6069
    Number of Reflections(R-Free) 166
    Number of Reflections(R-Work) 1226
    R-Factor(R-Work) 0.117
    R-Factor(R-Free) 0.1503
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6069
    Shell Resolution(Low) 4.755
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 1266
    R-Factor(R-Work) 0.1197
    R-Factor(R-Free) 0.1706
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.755
    Shell Resolution(Low) 4.9242
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 1263
    R-Factor(R-Work) 0.1239
    R-Factor(R-Free) 0.1648
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9242
    Shell Resolution(Low) 5.1204
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 1275
    R-Factor(R-Work) 0.1407
    R-Factor(R-Free) 0.1797
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1204
    Shell Resolution(Low) 5.3521
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 1282
    R-Factor(R-Work) 0.1437
    R-Factor(R-Free) 0.2172
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.3521
    Shell Resolution(Low) 5.6324
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 1242
    R-Factor(R-Work) 0.1563
    R-Factor(R-Free) 0.2234
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.6324
    Shell Resolution(Low) 5.9825
    Number of Reflections(R-Free) 158
    Number of Reflections(R-Work) 1248
    R-Factor(R-Work) 0.173
    R-Factor(R-Free) 0.209
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.9825
    Shell Resolution(Low) 6.44
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 1299
    R-Factor(R-Work) 0.176
    R-Factor(R-Free) 0.2271
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.44
    Shell Resolution(Low) 7.0798
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 1251
    R-Factor(R-Work) 0.1713
    R-Factor(R-Free) 0.2336
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.0798
    Shell Resolution(Low) 8.0856
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 1271
    R-Factor(R-Work) 0.1702
    R-Factor(R-Free) 0.2027
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.0856
    Shell Resolution(Low) 10.1176
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 1153
    R-Factor(R-Work) 0.1678
    R-Factor(R-Free) 0.1685
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 10.1176
    Shell Resolution(Low) 29.4043
    Number of Reflections(R-Free) 73
    Number of Reflections(R-Work) 637
    R-Factor(R-Work) 0.2486
    R-Factor(R-Free) 0.2285
    Percent Reflections(Observed) 50.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 20.231
    f_plane_restr 0.006
    f_chiral_restr 0.082
    f_angle_d 1.295
    f_bond_d 0.027
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 10079
    Nucleic Acid Atoms 730
    Heterogen Atoms 2
    Solvent Atoms 7
     
     
  •   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