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X-RAY DIFFRACTION
Materials and Methods page
4GSK
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 6.7
    Temperature 294.0
    Details 76.5 mM sodium/potassium phosphate, pH 6.5, 9 mM Tris, pH 8.5, 153 mM sodium chloride, 100 mM glycine, 72 mM sodium/potassium tartrate, 19.125% PEG1000, 0.045% PEG5000 MME, 4.5% dioxane, VAPOR DIFFUSION, SITTING DROP, temperature 294K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 120.56 α = 90
    b = 146.19 β = 90
    c = 108.44 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2012-03-29
     
    Diffraction Radiation
    Monochromator double crystal Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 24-ID-C
    Wavelength List 0.9795
    Site APS
    Beamline 24-ID-C
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.9
    Resolution(Low) 50
    Number Reflections(All) 43151
    Number Reflections(Observed) 42754
    Percent Possible(Observed) 99.1
    R Merge I(Observed) 0.134
    Redundancy 3.2
     
    High Resolution Shell Details
    Resolution(High) 2.9
    Resolution(Low) 3.0
    Percent Possible(All) 99.3
    R Merge I(Observed) 0.765
    Redundancy 3.3
    Number Unique Reflections(All) 4226
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.9
    Resolution(Low) 49.565
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 43201
    Number of Reflections(Observed) 42709
    Number of Reflections(R-Free) 2154
    Percent Reflections(Observed) 98.9
    R-Factor(All) 0.2387
    R-Factor(Observed) 0.2387
    R-Work 0.2362
    R-Free 0.2855
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 79.6706
    Anisotropic B[1][1] -27.8803
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -2.9421
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -30.4193
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9
    Shell Resolution(Low) 2.9676
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2594
    R-Factor(R-Work) 0.3099
    R-Factor(R-Free) 0.3565
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9676
    Shell Resolution(Low) 3.0418
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2697
    R-Factor(R-Work) 0.3189
    R-Factor(R-Free) 0.3563
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0418
    Shell Resolution(Low) 3.124
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2658
    R-Factor(R-Work) 0.3047
    R-Factor(R-Free) 0.3783
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.124
    Shell Resolution(Low) 3.216
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2665
    R-Factor(R-Work) 0.2936
    R-Factor(R-Free) 0.3466
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.216
    Shell Resolution(Low) 3.3197
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2673
    R-Factor(R-Work) 0.2802
    R-Factor(R-Free) 0.3085
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3197
    Shell Resolution(Low) 3.4384
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2661
    R-Factor(R-Work) 0.2643
    R-Factor(R-Free) 0.3148
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4384
    Shell Resolution(Low) 3.576
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2674
    R-Factor(R-Work) 0.2517
    R-Factor(R-Free) 0.3084
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.576
    Shell Resolution(Low) 3.7387
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2678
    R-Factor(R-Work) 0.2296
    R-Factor(R-Free) 0.3136
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7387
    Shell Resolution(Low) 3.9357
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2675
    R-Factor(R-Work) 0.2311
    R-Factor(R-Free) 0.2796
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9357
    Shell Resolution(Low) 4.1822
    Number of Reflections(R-Free) 128
    Number of Reflections(R-Work) 2744
    R-Factor(R-Work) 0.2131
    R-Factor(R-Free) 0.2409
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1822
    Shell Resolution(Low) 4.5049
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2691
    R-Factor(R-Work) 0.1997
    R-Factor(R-Free) 0.2442
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5049
    Shell Resolution(Low) 4.9579
    Number of Reflections(R-Free) 117
    Number of Reflections(R-Work) 2738
    R-Factor(R-Work) 0.1937
    R-Factor(R-Free) 0.243
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9579
    Shell Resolution(Low) 5.6744
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2744
    R-Factor(R-Work) 0.2196
    R-Factor(R-Free) 0.2536
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.6744
    Shell Resolution(Low) 7.1457
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2767
    R-Factor(R-Work) 0.2723
    R-Factor(R-Free) 0.3461
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.1457
    Shell Resolution(Low) 49.5722
    Number of Reflections(R-Free) 161
    Number of Reflections(R-Work) 2896
    R-Factor(R-Work) 0.2076
    R-Factor(R-Free) 0.2481
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 13.874
    f_plane_restr 0.004
    f_chiral_restr 0.063
    f_angle_d 0.842
    f_bond_d 0.004
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 11406
    Nucleic Acid Atoms 0
    Heterogen Atoms 2
    Solvent Atoms 0
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution Phaser
    Structure Refinement PHENIX (phenix.refine: dev_1000)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction HKL