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Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 5.0mg/ml of PDE4D-UCR2 (CID7620) + 0.5mM BPN5004 against 8.75% w/v PEG1,000, 6.25% w/v PEG3,350, 6.25% w/v MPD, 0.015M NPS (sodium nitrate, disodium hydrogen phosphate, ammonium sulfate), 0.05M MOPS/HEPES-Na pH 7.5, 20% v/v ethanol, 0.05M Phosphate-citrate pH 4.2
Crystal Properties Matthews coefficient Solvent content 2.16 43.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.78 α = 90 b = 81.89 β = 110.41 c = 116.79 γ = 90
Symmetry Space Group P 1 21 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 300 mm CCD 2012-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.7 50 97.3 0.085 11.85 5.2 154546 -3 27.18
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.74 95.8 0.499 3 5.1
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.7 45.5 154544 7761 97.4 0.162 0.161 0.1725 0.186 0.1984 RANDOM 21.14
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] 0.27 -0.93 0.73 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.372 r_dihedral_angle_4_deg 19.086 r_dihedral_angle_3_deg 12.949 r_dihedral_angle_1_deg 5.028 r_angle_refined_deg 1.408 r_angle_other_deg 1.216 r_chiral_restr 0.088 r_bond_refined_d 0.014 r_bond_other_d 0.008 r_gen_planes_refined 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.372 r_dihedral_angle_4_deg 19.086 r_dihedral_angle_3_deg 12.949 r_dihedral_angle_1_deg 5.028 r_angle_refined_deg 1.408 r_angle_other_deg 1.216 r_chiral_restr 0.088 r_bond_refined_d 0.014 r_bond_other_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.005 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10567 Nucleic Acid Atoms Solvent Atoms 1132 Heterogen Atoms 134
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC refinement