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crystal structure of yeast caPDE2 in complex with IBMX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 297 The 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 coefficient Solvent content 2.39 48.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.19 α = 90 b = 73.639 β = 108.49 c = 64.954 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2017-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.9 65.53 97.4 14.5 7.2 47636
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 1.9 65.53 45302 2333 96.88 0.19083 0.18968 0.21294 0.2162 RANDOM 36.301
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.135 r_dihedral_angle_4_deg 13.189 r_dihedral_angle_3_deg 12.028 r_dihedral_angle_1_deg 5.121 r_long_range_B_refined 4.52 r_long_range_B_other 4.445 r_scangle_other 2.672 r_mcangle_it 2.389 r_mcangle_other 2.389 r_scbond_it 1.578
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.135 r_dihedral_angle_4_deg 13.189 r_dihedral_angle_3_deg 12.028 r_dihedral_angle_1_deg 5.121 r_long_range_B_refined 4.52 r_long_range_B_other 4.445 r_scangle_other 2.672 r_mcangle_it 2.389 r_mcangle_other 2.389 r_scbond_it 1.578 r_scbond_other 1.578 r_mcbond_it 1.443 r_mcbond_other 1.442 r_angle_refined_deg 0.976 r_angle_other_deg 0.718 r_chiral_restr 0.058 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 4208 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing