3IBJ

X-ray structure of PDE2A


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION277Purified PDE2(215-900) was exchanged into crystallization buffer (50 mM HEPES pH7.5, 50 mM NaCl, and 2 mM TCEP) to a final concentration of 10mg/ml. Protein was mixed 1:1 with precipitant solution composed of 5-10% isopropanol, 0.1 M MES pH5.4-6.0, 0.2M Ca(OAc)2. Clusters of thin plate-like crystals appeared in 3-4 days, VAPOR DIFFUSION, temperature 277K
Crystal Properties
Matthew coefficientSolvent content
2.4850.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.233α = 90
b = 89.699β = 90
c = 264.187γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2006-10-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-41.28ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
135099.80.14128.5714.23187231809-393.975
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
33.11100

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1MC0; 1Z1L3.0218.2631511159899.510.21470.20960.311RANDOM77.62
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]
-17.26543983-10.1737505927.43919042
RMS Deviations
KeyRefinement Restraint Deviation
t_dihedral_angle_d30.704
t_it2.303
t_angle_deg1.381
t_nbd0.064
t_gen_planes0.015
t_trig_c_planes0.012
t_bond_d0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10455
Nucleic Acid Atoms
Solvent Atoms191
Heterogen Atoms4

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
BUSTER-TNTrefinement
HKL-2000data reduction
HKL-2000data scaling