6CPT

crystal structure of yeast caPDE2 in complex with IBMX


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP297The 10-15 mg/ml full length caPDE2 (1-571) was stored in a buffer of 20 mM Tris.base, pH 7.5, 50 mM NaCl, 1 mM 2-mercaptoethanol, 1 mM EDTA and crystallized at room temperature by hanging drop against a well buffer of 50 mM MES, pH 6.5, 0.1 M ammonium sulfate, 6-10% PEG8000, or a buffer of 50 mM Na citrate pH 5.6, 0.1 M ammonium acetate, 5% glycerol, and 6-10% PEG3350. The caPDE2-IBMX complex was prepared by soaking the native crystal s in the crystallization buffer with 10 mM IBMX
Crystal Properties
Matthews coefficientSolvent content
2.3948.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 138.19α = 90
b = 73.639β = 108.49
c = 64.954γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2017-10-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1APS22-BM

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
11.965.5397.414.57.247636
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.93

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONTHROUGHOUT1.965.5345302233396.880.190830.189680.21294RANDOM36.301
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.135
r_dihedral_angle_4_deg13.189
r_dihedral_angle_3_deg12.028
r_dihedral_angle_1_deg5.121
r_long_range_B_refined4.52
r_long_range_B_other4.445
r_scangle_other2.672
r_mcangle_it2.389
r_mcangle_other2.389
r_scbond_it1.578
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.135
r_dihedral_angle_4_deg13.189
r_dihedral_angle_3_deg12.028
r_dihedral_angle_1_deg5.121
r_long_range_B_refined4.52
r_long_range_B_other4.445
r_scangle_other2.672
r_mcangle_it2.389
r_mcangle_other2.389
r_scbond_it1.578
r_scbond_other1.578
r_mcbond_it1.443
r_mcbond_other1.442
r_angle_refined_deg0.976
r_angle_other_deg0.718
r_chiral_restr0.058
r_bond_refined_d0.005
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4208
Nucleic Acid Atoms
Solvent Atoms185
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing