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X-RAY DIFFRACTION
Materials and Methods page
4GX7
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5.5
    Temperature 298.0
    Details 0.1 M ammonium acetate, 0.1 M Bis-tris, 25% PEG 3350, 30 mM Me-alpha-mannose, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 99.77 α = 90
    b = 99.77 β = 90
    c = 172.37 γ = 120
     
    Space Group
    Space Group Name:    P 31 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type OXFORD ONYX CCD
    Collection Date 2012-01-30
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SEALED TUBE
    Type OTHER
    Wavelength List 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.85
    Resolution(Low) 24.9
    Number Reflections(All) 23789
    Number Reflections(Observed) 23789
    Percent Possible(Observed) 99.8
    Redundancy 4.9
     
    High Resolution Shell Details
    Resolution(High) 2.85
    Resolution(Low) 3.0
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.477
    Mean I Over Sigma(Observed) 1.5
    R-Sym I(Observed) 0.477
    Redundancy 4.9
    Number Unique Reflections(All) 3401
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.85
    Resolution(Low) 24.895
    Cut-off Sigma(F) 1.35
    Number of Reflections(Observed) 23763
    Number of Reflections(R-Free) 1182
    Percent Reflections(Observed) 99.95
    R-Factor(Observed) 0.1973
    R-Work 0.1946
    R-Free 0.2481
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 24.7374
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.85
    Shell Resolution(Low) 2.9796
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2777
    R-Factor(R-Work) 0.2417
    R-Factor(R-Free) 0.3075
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9796
    Shell Resolution(Low) 3.1364
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2775
    R-Factor(R-Work) 0.2428
    R-Factor(R-Free) 0.3027
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1364
    Shell Resolution(Low) 3.3324
    Number of Reflections(R-Free) 159
    Number of Reflections(R-Work) 2777
    R-Factor(R-Work) 0.2208
    R-Factor(R-Free) 0.2875
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3324
    Shell Resolution(Low) 3.589
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2802
    R-Factor(R-Work) 0.1982
    R-Factor(R-Free) 0.2745
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.589
    Shell Resolution(Low) 3.9489
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 2796
    R-Factor(R-Work) 0.1805
    R-Factor(R-Free) 0.2506
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9489
    Shell Resolution(Low) 4.5174
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2823
    R-Factor(R-Work) 0.1631
    R-Factor(R-Free) 0.2013
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5174
    Shell Resolution(Low) 5.6803
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2863
    R-Factor(R-Work) 0.1617
    R-Factor(R-Free) 0.1983
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.6803
    Shell Resolution(Low) 24.8957
    Number of Reflections(R-Free) 158
    Number of Reflections(R-Work) 2968
    R-Factor(R-Work) 0.2013
    R-Factor(R-Free) 0.2269
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 14.392
    f_plane_restr 0.004
    f_chiral_restr 0.058
    f_angle_d 1.045
    f_bond_d 0.005
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 5775
    Nucleic Acid Atoms 0
    Heterogen Atoms 78
    Solvent Atoms 0
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) d*TREK
    Data Reduction (data scaling) SCALA
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.8_1069)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    molecular replacement Phaser version: 2.3.0
    data reduction SCALA version: 3.3.20
    data collection D*trek