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An Information Portal to 107049 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4GDK
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.5
    Temperature 293.0
    Details PROTEIN: 10 MG/ML in 0.01M HEPES pH 7.0, 0.3 M NaCl, 0.001 M DTT; RESERVOIR: 0.1M Hepes pH7.5, 0.2 M lithium citrate, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 43.76 α = 90
    b = 113.15 β = 90
    c = 210.68 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 MARMOSAIC 225 mm CCD
    Collection Date 2009-08-16
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 22-BM
    Wavelength List 1.0000
    Site APS
    Beamline 22-BM
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.7
    Resolution(Low) 50
    Number Reflections(Observed) 29676
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.1
    Redundancy 6.9
     
    High Resolution Shell Details
    Resolution(High) 2.7
    Resolution(Low) 2.8
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.636
    Redundancy 6.1
    Number Unique Reflections(All) 2866
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.7
    Resolution(Low) 44.058
    Cut-off Sigma(F) 1.34
    Number of Reflections(Observed) 29598
    Number of Reflections(R-Free) 2000
    Percent Reflections(Observed) 99.5
    R-Factor(Observed) 0.1796
    R-Work 0.1756
    R-Free 0.2361
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 67.2963
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6999
    Shell Resolution(Low) 2.7674
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 1821
    R-Factor(R-Work) 0.2435
    R-Factor(R-Free) 0.2957
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7674
    Shell Resolution(Low) 2.8422
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 1927
    R-Factor(R-Work) 0.2411
    R-Factor(R-Free) 0.3039
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8422
    Shell Resolution(Low) 2.9258
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 1963
    R-Factor(R-Work) 0.2394
    R-Factor(R-Free) 0.3327
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9258
    Shell Resolution(Low) 3.0202
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 1903
    R-Factor(R-Work) 0.2343
    R-Factor(R-Free) 0.2766
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0202
    Shell Resolution(Low) 3.1281
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 1988
    R-Factor(R-Work) 0.2289
    R-Factor(R-Free) 0.2932
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1281
    Shell Resolution(Low) 3.2533
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 1927
    R-Factor(R-Work) 0.2129
    R-Factor(R-Free) 0.312
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2533
    Shell Resolution(Low) 3.4014
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 1985
    R-Factor(R-Work) 0.2083
    R-Factor(R-Free) 0.2762
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4014
    Shell Resolution(Low) 3.5806
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 1949
    R-Factor(R-Work) 0.1983
    R-Factor(R-Free) 0.2264
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5806
    Shell Resolution(Low) 3.8048
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 1963
    R-Factor(R-Work) 0.1753
    R-Factor(R-Free) 0.2476
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8048
    Shell Resolution(Low) 4.0984
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 1975
    R-Factor(R-Work) 0.1614
    R-Factor(R-Free) 0.2335
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0984
    Shell Resolution(Low) 4.5105
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2003
    R-Factor(R-Work) 0.1379
    R-Factor(R-Free) 0.2014
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5105
    Shell Resolution(Low) 5.1623
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 1999
    R-Factor(R-Work) 0.1299
    R-Factor(R-Free) 0.197
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1623
    Shell Resolution(Low) 6.5006
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2044
    R-Factor(R-Work) 0.1667
    R-Factor(R-Free) 0.233
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.5006
    Shell Resolution(Low) 44.0639
    Number of Reflections(R-Free) 156
    Number of Reflections(R-Work) 2151
    R-Factor(R-Work) 0.1661
    R-Factor(R-Free) 0.1963
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 11.391
    f_plane_restr 0.003
    f_chiral_restr 0.049
    f_angle_d 0.661
    f_bond_d 0.003
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 6469
    Nucleic Acid Atoms 0
    Heterogen Atoms 2
    Solvent Atoms 76
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) HKL
    Data Reduction (data scaling) HKL
    Structure Refinement PHENIX (phenix.refine: 1.8_1069)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction HKL