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X-RAY DIFFRACTION
Materials and Methods page
4I50
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 6.7
    Temperature 293.0
    Details 3% PEG 4000, 4-6% glycerol, 30 mM magnesium chloride, 30 mM calcium chloride, 100 mM MES/Imidazole, pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 103.62 α = 90
    b = 155.13 β = 90
    c = 180.41 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector PIXEL
    Type DECTRIS PILATUS 6M
    Collection Date 2012-04-25
     
    Diffraction Radiation
    Monochromator LN2 cooled fixed-exit Si(111) monochromator, Sagittally - horizontally focussed
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SLS BEAMLINE X06SA
    Wavelength List 1.00001
    Site SLS
    Beamline X06SA
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.3
    Resolution(Low) 77.6
    Number Reflections(All) 129393
    Number Reflections(Observed) 129393
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.133
    B(Isotropic) From Wilson Plot 50.3
    Redundancy 13.6
     
    High Resolution Shell Details
    Resolution(High) 2.3
    Resolution(Low) 2.36
    Percent Possible(All) 100.0
    Mean I Over Sigma(Observed) 1.17
    Redundancy 13.8
    Number Unique Reflections(All) 9467
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.3
    Resolution(Low) 77.565
    Cut-off Sigma(F) 1.99
    Number of Reflections(all) 129393
    Number of Reflections(Observed) 129379
    Number of Reflections(R-Free) 6505
    Percent Reflections(Observed) 99.99
    R-Factor(All) 0.1935
    R-Factor(Observed) 0.1935
    R-Work 0.1907
    R-Free 0.2463
     
    Temperature Factor Modeling
    Anisotropic B[1][1] 1.6336
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 11.8387
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -5.8897
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3
    Shell Resolution(Low) 2.3261
    Number of Reflections(R-Free) 197
    Number of Reflections(R-Work) 4010
    R-Factor(R-Work) 0.3477
    R-Factor(R-Free) 0.4087
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3261
    Shell Resolution(Low) 2.3535
    Number of Reflections(R-Free) 239
    Number of Reflections(R-Work) 4090
    R-Factor(R-Work) 0.3172
    R-Factor(R-Free) 0.3742
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3535
    Shell Resolution(Low) 2.3822
    Number of Reflections(R-Free) 241
    Number of Reflections(R-Work) 3984
    R-Factor(R-Work) 0.2973
    R-Factor(R-Free) 0.3511
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3822
    Shell Resolution(Low) 2.4123
    Number of Reflections(R-Free) 194
    Number of Reflections(R-Work) 4091
    R-Factor(R-Work) 0.2856
    R-Factor(R-Free) 0.3264
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4123
    Shell Resolution(Low) 2.4441
    Number of Reflections(R-Free) 236
    Number of Reflections(R-Work) 4016
    R-Factor(R-Work) 0.28
    R-Factor(R-Free) 0.3501
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4441
    Shell Resolution(Low) 2.4775
    Number of Reflections(R-Free) 209
    Number of Reflections(R-Work) 4089
    R-Factor(R-Work) 0.283
    R-Factor(R-Free) 0.3551
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4775
    Shell Resolution(Low) 2.5129
    Number of Reflections(R-Free) 215
    Number of Reflections(R-Work) 4042
    R-Factor(R-Work) 0.2685
    R-Factor(R-Free) 0.3279
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5129
    Shell Resolution(Low) 2.5505
    Number of Reflections(R-Free) 205
    Number of Reflections(R-Work) 4059
    R-Factor(R-Work) 0.2642
    R-Factor(R-Free) 0.3275
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5505
    Shell Resolution(Low) 2.5903
    Number of Reflections(R-Free) 198
    Number of Reflections(R-Work) 4138
    R-Factor(R-Work) 0.242
    R-Factor(R-Free) 0.325
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5903
    Shell Resolution(Low) 2.6328
    Number of Reflections(R-Free) 219
    Number of Reflections(R-Work) 3985
    R-Factor(R-Work) 0.243
    R-Factor(R-Free) 0.3175
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6328
    Shell Resolution(Low) 2.6782
    Number of Reflections(R-Free) 205
    Number of Reflections(R-Work) 4102
    R-Factor(R-Work) 0.2484
    R-Factor(R-Free) 0.3042
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6782
    Shell Resolution(Low) 2.7269
    Number of Reflections(R-Free) 211
    Number of Reflections(R-Work) 4096
    R-Factor(R-Work) 0.2408
    R-Factor(R-Free) 0.3087
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7269
    Shell Resolution(Low) 2.7793
    Number of Reflections(R-Free) 213
    Number of Reflections(R-Work) 4028
    R-Factor(R-Work) 0.2252
    R-Factor(R-Free) 0.2995
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7793
    Shell Resolution(Low) 2.8361
    Number of Reflections(R-Free) 238
    Number of Reflections(R-Work) 4036
    R-Factor(R-Work) 0.2175
    R-Factor(R-Free) 0.32
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8361
    Shell Resolution(Low) 2.8977
    Number of Reflections(R-Free) 232
    Number of Reflections(R-Work) 4096
    R-Factor(R-Work) 0.2072
    R-Factor(R-Free) 0.2747
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8977
    Shell Resolution(Low) 2.9651
    Number of Reflections(R-Free) 223
    Number of Reflections(R-Work) 4062
    R-Factor(R-Work) 0.2079
    R-Factor(R-Free) 0.2755
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9651
    Shell Resolution(Low) 3.0393
    Number of Reflections(R-Free) 225
    Number of Reflections(R-Work) 4050
    R-Factor(R-Work) 0.1997
    R-Factor(R-Free) 0.2532
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0393
    Shell Resolution(Low) 3.1215
    Number of Reflections(R-Free) 216
    Number of Reflections(R-Work) 4093
    R-Factor(R-Work) 0.1982
    R-Factor(R-Free) 0.2833
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1215
    Shell Resolution(Low) 3.2133
    Number of Reflections(R-Free) 215
    Number of Reflections(R-Work) 4091
    R-Factor(R-Work) 0.2054
    R-Factor(R-Free) 0.2887
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2133
    Shell Resolution(Low) 3.317
    Number of Reflections(R-Free) 189
    Number of Reflections(R-Work) 4115
    R-Factor(R-Work) 0.2037
    R-Factor(R-Free) 0.2774
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.317
    Shell Resolution(Low) 3.4356
    Number of Reflections(R-Free) 213
    Number of Reflections(R-Work) 4092
    R-Factor(R-Work) 0.1937
    R-Factor(R-Free) 0.2455
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4356
    Shell Resolution(Low) 3.5732
    Number of Reflections(R-Free) 197
    Number of Reflections(R-Work) 4127
    R-Factor(R-Work) 0.1818
    R-Factor(R-Free) 0.2447
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5732
    Shell Resolution(Low) 3.7358
    Number of Reflections(R-Free) 219
    Number of Reflections(R-Work) 4090
    R-Factor(R-Work) 0.1802
    R-Factor(R-Free) 0.2287
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7358
    Shell Resolution(Low) 3.9327
    Number of Reflections(R-Free) 205
    Number of Reflections(R-Work) 4124
    R-Factor(R-Work) 0.1703
    R-Factor(R-Free) 0.2377
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9327
    Shell Resolution(Low) 4.1791
    Number of Reflections(R-Free) 219
    Number of Reflections(R-Work) 4136
    R-Factor(R-Work) 0.1579
    R-Factor(R-Free) 0.2121
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1791
    Shell Resolution(Low) 4.5017
    Number of Reflections(R-Free) 247
    Number of Reflections(R-Work) 4108
    R-Factor(R-Work) 0.1435
    R-Factor(R-Free) 0.1973
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5017
    Shell Resolution(Low) 4.9547
    Number of Reflections(R-Free) 215
    Number of Reflections(R-Work) 4157
    R-Factor(R-Work) 0.1336
    R-Factor(R-Free) 0.1814
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9547
    Shell Resolution(Low) 5.6715
    Number of Reflections(R-Free) 216
    Number of Reflections(R-Work) 4169
    R-Factor(R-Work) 0.1688
    R-Factor(R-Free) 0.2172
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.6715
    Shell Resolution(Low) 7.1447
    Number of Reflections(R-Free) 225
    Number of Reflections(R-Work) 4211
    R-Factor(R-Work) 0.1933
    R-Factor(R-Free) 0.262
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.1447
    Shell Resolution(Low) 77.6091
    Number of Reflections(R-Free) 229
    Number of Reflections(R-Work) 4387
    R-Factor(R-Work) 0.1792
    R-Factor(R-Free) 0.1924
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.004
    f_chiral_restr 0.051
    f_dihedral_angle_d 15.184
    f_angle_d 0.943
    f_bond_d 0.005
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 17039
    Nucleic Acid Atoms 0
    Heterogen Atoms 240
    Solvent Atoms 306
     
     
  •   Software and Computing Hide
    Computing
    Data Collection REMDAQ
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XDS
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.7.3_928)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7.3_928)
    model building PHASER
    data collection REMDAQ