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An Information Portal to 105339 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4GH6
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.5
    Temperature 298.0
    Details PDE9A2 (15 mg/mL) in a buffer of 50 mM NaCl, 20 mM Tris.HCl pH 7.5, 1 mM beta-mercaptoethanol and 1 mM EDTA was mixed with 2 mM IBMX for 2h before setting-up of crystallization against the well buffer of 2.0 M Na formate, 0.1 M HEPES pH 7.5, 5% xylitol at 4C. The PDE9A-IBMX complex crystals were formed after 1d and reached the maximum size in 2 weeks. Crystals of the PDE9A-28 complex were prepared by soaking PDE9-IBMX co-crystals in the crystallization buffer plus 5 mM 28 at 25C for 3 days, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 104.28 α = 90
    b = 104.28 β = 90
    c = 270.07 γ = 90
     
    Space Group
    Space Group Name:    P 41 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type PHOTON FACTORY BEAMLINE BL-17A
    Wavelength List 1.0
    Site PHOTON FACTORY
    Beamline BL-17A
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.7
    Resolution(Low) 30
    Number Reflections(Observed) 41120
    Percent Possible(Observed) 99.7
    R Merge I(Observed) 0.093
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.7
    Resolution(Low) 30.0
    Cut-off Sigma(I) 0.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 38971
    Number of Reflections(R-Free) 3897
    R-Work 0.212
    R-Free 0.245
    R-Free Selection Details Random
     
    Temperature Factor Modeling
    Isotropic Thermal Model isotropic
    Mean Isotropic B Value 52.8
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_bond_d 0.007
    c_angle_deg 1.3
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 5390
    Nucleic Acid Atoms 0
    Heterogen Atoms 97
    Solvent Atoms 18
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution AMoRE
    Structure Refinement CNS1.2
     
    Software
    refinement CNS1.2
    model building AMoRE