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X-RAY DIFFRACTION
Materials and Methods page
3M08
  •   Crystallization Hide
    Crystallization Experiments
    Method sitting drop
    pH 6.5
    Temperature 298.0
    Details 15% PEG 6000, 0.15 M sodium acetate, 0.1M MES buffer, pH 6.5, sitting drop, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 79.18 α = 90
    b = 79.18 β = 90
    c = 107.89 γ = 120
     
    Space Group
    Space Group Name:    P 61 2 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector IMAGE PLATE
    Type RIGAKU RAXIS IV++
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU RUH3R
    Wavelength List 1.54
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.01
    Resolution(Low) 42.4
    Number Reflections(All) 13728
    Number Reflections(Observed) 13728
    Percent Possible(Observed) 99.5
    Redundancy 5.1
     
    High Resolution Shell Details
    Resolution(High) 2.014
    Resolution(Low) 2.12
    Percent Possible(All) 98.7
    R Merge I(Observed) 0.118
    Mean I Over Sigma(Observed) 5.8
    R-Sym I(Observed) 0.118
    Redundancy 5.1
    Number Unique Reflections(All) 1918
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.014
    Resolution(Low) 31.849
    Cut-off Sigma(F) 0.01
    Number of Reflections(Observed) 13579
    Number of Reflections(R-Free) 1366
    Percent Reflections(Observed) 98.41
    R-Factor(Observed) 0.179
    R-Work 0.175
    R-Free 0.213
     
    Temperature Factor Modeling
    Mean Isotropic B Value 19.978
    Anisotropic B[1][1] -0.782
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.782
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 1.563
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.014
    Shell Resolution(Low) 2.086
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 1163
    R-Factor(R-Work) 0.189
    R-Factor(R-Free) 0.291
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.086
    Shell Resolution(Low) 2.17
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 1152
    R-Factor(R-Work) 0.166
    R-Factor(R-Free) 0.191
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.17
    Shell Resolution(Low) 2.268
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 1194
    R-Factor(R-Work) 0.159
    R-Factor(R-Free) 0.225
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.268
    Shell Resolution(Low) 2.388
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 1181
    R-Factor(R-Work) 0.166
    R-Factor(R-Free) 0.223
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.388
    Shell Resolution(Low) 2.537
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 1199
    R-Factor(R-Work) 0.165
    R-Factor(R-Free) 0.211
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.537
    Shell Resolution(Low) 2.733
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 1224
    R-Factor(R-Work) 0.178
    R-Factor(R-Free) 0.197
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.733
    Shell Resolution(Low) 3.008
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 1221
    R-Factor(R-Work) 0.176
    R-Factor(R-Free) 0.226
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.008
    Shell Resolution(Low) 3.443
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 1253
    R-Factor(R-Work) 0.173
    R-Factor(R-Free) 0.207
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.443
    Shell Resolution(Low) 4.336
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 1268
    R-Factor(R-Work) 0.155
    R-Factor(R-Free) 0.186
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.336
    Shell Resolution(Low) 31.853
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 1358
    R-Factor(R-Work) 0.179
    R-Factor(R-Free) 0.203
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 28.591
    f_plane_restr 0.007
    f_chiral_restr 0.081
    f_angle_d 1.034
    f_bond_d 0.005
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1290
    Nucleic Acid Atoms 0
    Heterogen Atoms 90
    Solvent Atoms 171
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.5_2)
     
    Software
    data extraction pdb_extract version: 3.005
    refinement phenix
    molecular replacement Phaser version: 2.1.1
    data processing SCALA version: 3.3.15
    reflection data processing Mosflm