☰ Navigation Tabs
Crystal structure of PDE4D catalytic domain complexed with compound 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WQA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.4 277 0.1 M HEPES (pH 7.4), 0.1 M MgCl2, 15-20% PE G3350, 10% isopropanol, 25% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.55 51.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.311 α = 90 b = 79.7 β = 90 c = 163.316 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 CCD OXFORD ONYX CCD 2018-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION NOVA 1.5418
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 2.2 22.15 99 0.052 23.4 3.6 40198 27.1812120528
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 2.2 2.28 98.3 0.347 2.16 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5WQA 2.20000094865 22.1481461147 1.370723182 39757 1910 99.2089634177 0.203477361054 0.201308334149 0.2026 0.246253774685 0.247 34.2062049023
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.3927422413 f_angle_d 0.870883925101 f_chiral_restr 0.0449258933089 f_bond_d 0.00768954804932 f_plane_restr 0.00559397320162
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5303 Nucleic Acid Atoms Solvent Atoms 278 Heterogen Atoms 64
Software Software Software Name Purpose PHENIX refinement CrysalisPro data reduction CrysalisPro data scaling PHASER phasing