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Crystal structure of the catalytic domain of PDE4D2 with compound 12c
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 294 20% PEG 3350, 25% (v/v) ethylene glycol, 10% (v/v) isopropanol, 100 mM HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.93 58.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.54 α = 90 b = 111.2 β = 90 c = 160.95 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 IMAGE PLATE RIGAKU RAXIS IV MIRRORS 2011-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE 1.54
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 67.36 98.1 0.078 9.8 4.45 89513 2 2
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 88.7 0.381 2.3 2.29 7982
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 Molrep 2.44 65.19 0.02 66827 66493 3367 99.05 0.201 0.1981 0.2561 0.2561 RANDOM 44.3798
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] 1.0886 -1.827 0.7384
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 19.801 f_angle_d 1.073 f_chiral_restr 0.073 f_bond_d 0.008 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10531 Nucleic Acid Atoms Solvent Atoms 220 Heterogen Atoms 271
Software Software Software Name Purpose d*TREK data scaling d*TREK data reduction PHENIX refinement PDB_EXTRACT data extraction CrystalClear data collection MOLREP phasing