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Crystal structure of PDE4D2 in complex with inhibitor LEO39652
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y2K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 Protein stored at 20.6 mg/mL in a storage buffer of 50 mM NaCl, 20 mM Tris HCl (pH 7.5), 1 mM TCEP, 1 mM EDTA. Reservoir was 0.1 M HEPES (pH 7.5), 19% PEG3350, 25% ethylene glycol, 5% 2-propanol, 5% glycerol. Drops were microseeded. Apo crystals were soaked with 0.8 mM LEO39652A for 3 days.
Crystal Properties Matthews coefficient Solvent content 2.7 54.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.03 α = 90 b = 111.866 β = 90 c = 159.623 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 X 9M 2019-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9159 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.6 79.939 100 0.085 0.997 9.2 6.6 235229
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 100 1.481 0.422 1 6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1Y2K 1.6 79.939 235038 11947 99.938 0.163 0.1616 0.1739 0.1918 0.2019 27.135
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] 0.009 -0.008 -0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.745 r_dihedral_angle_4_deg 16.941 r_dihedral_angle_3_deg 13.454 r_lrange_it 6.874 r_lrange_other 6.455 r_dihedral_angle_1_deg 5.423 r_scangle_it 4.972 r_scangle_other 4.971 r_scbond_it 3.319 r_scbond_other 3.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.745 r_dihedral_angle_4_deg 16.941 r_dihedral_angle_3_deg 13.454 r_lrange_it 6.874 r_lrange_other 6.455 r_dihedral_angle_1_deg 5.423 r_scangle_it 4.972 r_scangle_other 4.971 r_scbond_it 3.319 r_scbond_other 3.319 r_mcangle_it 2.804 r_mcangle_other 2.804 r_mcbond_it 2.157 r_mcbond_other 2.157 r_angle_refined_deg 1.59 r_angle_other_deg 1.521 r_nbd_other 0.243 r_xyhbond_nbd_refined 0.242 r_symmetry_xyhbond_nbd_refined 0.233 r_nbd_refined 0.231 r_symmetry_nbd_refined 0.217 r_symmetry_nbd_other 0.18 r_nbtor_refined 0.169 r_symmetry_xyhbond_nbd_other 0.136 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.082 r_metal_ion_refined 0.024 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10650 Nucleic Acid Atoms Solvent Atoms 1344 Heterogen Atoms 260
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing