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Synthesis and evaluation of heterocyclic catechol mimics as inhibitors of catechol-O-methyltransferase (COMT): Structure with Cmpd32 ([1-(biphenyl-3-yl)-5-hydroxy-4-oxo-1,4-dihydropyridin-3-yl]boronic acid)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XUC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 298 0.1M HEPES, 30% PEG 6000; MA000474 (JCSG core IV), drop e12 :100uM ligand, 12mg/ml protein
Crystal Properties Matthews coefficient Solvent content 2.56 51.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.812 α = 90 b = 57.631 β = 90 c = 98.249 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++ 2008-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 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 2.4 50 100 0.198 7.2 7.7 10266
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 2.4 2.44 100 0.696 7.7 505
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 MOLECULAR REPLACEMENT THROUGHOUT 4XUC 2.4 49.69 9611 484 98.66 0.1713 0.1679 0.167 0.241 0.2389 RANDOM 24.293
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] 1.66 -0.75 -0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.931 r_dihedral_angle_3_deg 13.893 r_dihedral_angle_4_deg 10.626 r_dihedral_angle_1_deg 5.734 r_scangle_it 2.743 r_scbond_it 1.681 r_angle_refined_deg 1.316 r_mcangle_it 1.025 r_mcbond_it 0.618 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.931 r_dihedral_angle_3_deg 13.893 r_dihedral_angle_4_deg 10.626 r_dihedral_angle_1_deg 5.734 r_scangle_it 2.743 r_scbond_it 1.681 r_angle_refined_deg 1.316 r_mcangle_it 1.025 r_mcbond_it 0.618 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.202 r_nbd_refined 0.188 r_symmetry_hbond_refined 0.184 r_xyhbond_nbd_refined 0.164 r_chiral_restr 0.084 r_metal_ion_refined 0.017 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1699 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 63
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing