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X-RAY DIFFRACTION
Materials and Methods page
4GSW
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5.5
    Temperature 291.0
    Details EhUbiquitin at 13 mg/mL in S200 buffer was mixed 1:1 with and equilibrated against crystallization solution containing 22% (w/v) PEG 3350, 200 mM LiSO4, and 100 mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 38.63 α = 90
    b = 49.87 β = 90
    c = 76.82 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 CCD
    Type MAR scanner 300 mm plate
    Collection Date 2012-04-08
     
    Diffraction Radiation
    Monochromator double crystal
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 23-ID-B
    Wavelength List 1.000
    Site APS
    Beamline 23-ID-B
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.15
    Resolution(Low) 40
    Number Reflections(All) 8593
    Number Reflections(Observed) 8430
    Percent Possible(Observed) 98.1
    R Merge I(Observed) 0.085
    B(Isotropic) From Wilson Plot 32.8
    Redundancy 3.5
     
    High Resolution Shell Details
    Resolution(High) 2.15
    Resolution(Low) 2.17
    Percent Possible(All) 96.8
    R Merge I(Observed) 0.279
    Mean I Over Sigma(Observed) 3.1
    Redundancy 3.3
    Number Unique Reflections(All) 210
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.15
    Resolution(Low) 34.513
    Cut-off Sigma(F) 1.34
    Number of Reflections(all) 8591
    Number of Reflections(Observed) 8379
    Number of Reflections(R-Free) 840
    Percent Reflections(Observed) 97.53
    R-Factor(Observed) 0.1994
    R-Work 0.1932
    R-Free 0.2561
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Data Not Available
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.15
    Shell Resolution(Low) 2.2772
    Number of Reflections(Observed) 1154
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 1154
    R-Factor(R-Work) 0.2658
    R-Factor(R-Free) 0.3505
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2772
    Shell Resolution(Low) 2.453
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 1213
    R-Factor(R-Work) 0.2456
    R-Factor(R-Free) 0.3471
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.453
    Shell Resolution(Low) 2.6997
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 1260
    R-Factor(R-Work) 0.2415
    R-Factor(R-Free) 0.3361
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6997
    Shell Resolution(Low) 3.0902
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 1276
    R-Factor(R-Work) 0.2206
    R-Factor(R-Free) 0.271
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0902
    Shell Resolution(Low) 3.8924
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 1293
    R-Factor(R-Work) 0.1768
    R-Factor(R-Free) 0.2642
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8924
    Shell Resolution(Low) 34.5176
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 1343
    R-Factor(R-Work) 0.1598
    R-Factor(R-Free) 0.193
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.007
    f_chiral_restr 0.094
    f_dihedral_angle_d 16.107
    f_angle_d 1.493
    f_bond_d 0.014
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1165
    Nucleic Acid Atoms 0
    Heterogen Atoms 10
    Solvent Atoms 44
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHENIX AutoMR
    Structure Refinement PHENIX (phenix.refine: 1.8_1069)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.8_1069)
    model building PHENIX version: AutoMR
    data collection HKL-2000