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Catalytic domain of human phosphodiesterase 4b2b in complex with a 5-heterocycle pyrazolopyridine inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D3P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 14-18% PEG 3000, 10% Glycerol, 50mM Sodium Cacodylate pH 6.5, 100mM Sodium Acetate, 1M Sodium Chloride, 1% DMF, 5mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.74 55.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.622 α = 90 b = 94.907 β = 90 c = 105.853 γ = 90
Symmetry Space Group I 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 210 2004-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
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 29.794 99.9 0.088 0.088 15 5.4 30473 30.3
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 2.11 99.9 0.519 0.519 1.1 5.4 4391
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 3D3P 2 20 30445 1537 100 0.1901 0.1874 0.1935 0.2399 0.2432 RANDOM 39.2292
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] -1.82 -1.19 3.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.277 r_dihedral_angle_4_deg 22.243 r_dihedral_angle_3_deg 15.331 r_scangle_it 5.653 r_dihedral_angle_1_deg 5.175 r_scbond_it 3.949 r_mcangle_it 3.125 r_mcbond_it 2.016 r_angle_refined_deg 1.406 r_angle_other_deg 0.986
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.277 r_dihedral_angle_4_deg 22.243 r_dihedral_angle_3_deg 15.331 r_scangle_it 5.653 r_dihedral_angle_1_deg 5.175 r_scbond_it 3.949 r_mcangle_it 3.125 r_mcbond_it 2.016 r_angle_refined_deg 1.406 r_angle_other_deg 0.986 r_mcbond_other 0.641 r_chiral_restr 0.098 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2711 Nucleic Acid Atoms Solvent Atoms 297 Heterogen Atoms 49
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction REFMAC phasing