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Selective Inhibition of the Catalytic Domain Of Human Phosphodiesterase 4B With A-33
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3G45 PDB entry 3G45
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 VCID6271 PDE4 AT 7.9 MG/ML IN 20MM HEPES PH 7.5, 100 MM NACL, 1MM DTT, WITH 0.5MM A-33 AGAINST JCSG_ A10 (OPTIMIZATION SCREEN), 328.57MM POTASSIUM FORMATE, 24% W/V PEG 3350, CRYO 20% ETHYLENE GLYCOL AND 0.1MM COMPOUND, CRYSTAL TRACKING ID 232128E12, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K, temperature 289.0K
Crystal Properties Matthews coefficient Solvent content 2.73 54.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.7 α = 90 b = 99.7 β = 90 c = 47.02 γ = 90
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 RIGAKU SATURN 944+ 2012-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 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 1.9 49.85 97.3 0.087 12.5 3.2 36759 35759 2 -3 18.71
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 1.9 1.95 86.7 0.483 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3G45 1.9 49.85 2 36759 35759 1788 97.3 0.19 0.188 0.1922 0.222 0.2241 RANDOM 12.8
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] 0.12 0.12 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.805 r_dihedral_angle_4_deg 19.018 r_dihedral_angle_3_deg 13.778 r_dihedral_angle_1_deg 5.002 r_angle_refined_deg 1.487 r_angle_other_deg 1.013 r_chiral_restr 0.084 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_gen_planes_other 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.805 r_dihedral_angle_4_deg 19.018 r_dihedral_angle_3_deg 13.778 r_dihedral_angle_1_deg 5.002 r_angle_refined_deg 1.487 r_angle_other_deg 1.013 r_chiral_restr 0.084 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_gen_planes_other 0.006 r_bond_other_d 0.003 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2758 Nucleic Acid Atoms Solvent Atoms 375 Heterogen Atoms 41
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling