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Three dimensional structures of PDE4D in complex with roliprams and implication on inhibitor selectivity
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F0J catalytic domain of PDE4B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 0.1 M HEPES, 20% PEG3350, 30% ethylene glycol, 10% isopropanol, and 5% glycerol , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.71 54.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.272 α = 90 b = 112.493 β = 90 c = 160.908 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 315 2002-03-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1 NSLS X25
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 2.3 99 97 0.053 14 6.3 77976
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) 2.3 2.38 75.6 0.246 2.8
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 catalytic domain of PDE4B 2.3 99 75736 7639 93.9 0.224 0.2234 0.259 0.2578 random 41.8
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] 0.316 0.005 -0.321
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 1.9 c_scbond_it 1.402 c_mcangle_it 1.383 c_angle_d 1.19 c_mcbond_it 0.802 c_bond_d 0.0062
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10718 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 88
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing CNS refinement