4OJX

crystal structure of yeast phosphodiesterase-1 in complex with GMP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5298The native crystal of yPDE1 (6 mg/ml) was grown by hanging drop against a buffer of 20 mM HEPES pH 7.5, 5% PEG3350, 40 mM Li sulfate, and 12% MPD at room temperature, or a similar buffer but 15% glycerol and 20% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4449.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.674α = 90
b = 85.162β = 90
c = 130.836γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152013-10-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.05NSLSX29A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.3134.3499.39826898268

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.3134.349826893308491099.520.168640.168060.17914RANDOM19.234
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.010.06-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.912
r_dihedral_angle_4_deg18.11
r_sphericity_free14.527
r_dihedral_angle_3_deg10.344
r_dihedral_angle_1_deg6.431
r_sphericity_bonded6.219
r_rigid_bond_restr2.588
r_angle_refined_deg1.25
r_chiral_restr0.086
r_bond_refined_d0.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.912
r_dihedral_angle_4_deg18.11
r_sphericity_free14.527
r_dihedral_angle_3_deg10.344
r_dihedral_angle_1_deg6.431
r_sphericity_bonded6.219
r_rigid_bond_restr2.588
r_angle_refined_deg1.25
r_chiral_restr0.086
r_bond_refined_d0.008
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2913
Nucleic Acid Atoms
Solvent Atoms215
Heterogen Atoms34

Software

Software
Software NamePurpose
ADSCdata collection
SOLVEphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling