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Crystal structure of the catalytic domain of PDE4D2 with (S)-N-(3-{1-[1-(3-Cyclopropylmethoxy-4-difluoromethoxyphenyl)-2-(1-oxypyridin-4-yl)-ethyl]-1H-pyrazl-3-yl}phenyl)acetamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SL8 PDB ENTRY 3SL8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 20% PEG 3350, 25%(v/v) ethylene glycol, 10%(v/v) isopropanol, 100mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.65 53.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.587 α = 90 b = 110.293 β = 90 c = 161.607 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 ADSC QUANTUM 210r 2005-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 6B 1.1 PAL/PLS 6B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.1 50 94.2 0.093 0.07 14.58 2.9 288261 97786 1 1 14.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.18 87.5 0.445 0.408 2.41 2.6 8984
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 3SL8 2.1 35.41 97786 91493 4581 88.6 0.208 0.206 0.206 0.1955 0.236 0.2271 RANDOM 28.4
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] 3.09 -7.91 4.81
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 18.7 c_scangle_it 3.09 c_scbond_it 2.14 c_mcangle_it 1.99 c_mcbond_it 1.29 c_angle_deg 1.056 c_improper_angle_d 0.78 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10596 Nucleic Acid Atoms Solvent Atoms 414 Heterogen Atoms 164
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling