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Crystal structures of rat Catechol-O-Methyltransferase complexed with coumarine-based inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VID PDB entry 1VID
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.2M (NH4)2SO4, 30% PEG 8000, 0.1M Tris pH7.5, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.47 50.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.448 α = 90 b = 50.448 β = 90 c = 167.626 γ = 120
Symmetry Space Group P 32 2 1
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 JUPITER 210 2004-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32B2 1.0 SPring-8 BL32B2
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 2.3 42.3 99.6 0.074 0.068 16.7 6.8 11635 11591 49.5
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 2.42 100 0.181 8.2 7.2 1644
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 PDB entry 1VID 2.3 42.3 10454 1134 99.64 0.2187 0.21147 0.213 0.28646 0.2846 RANDOM 41.807
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] 2.22 1.11 2.22 -3.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.27 r_dihedral_angle_4_deg 19.738 r_dihedral_angle_3_deg 17.589 r_dihedral_angle_1_deg 5.777 r_scangle_it 2.829 r_scbond_it 1.798 r_angle_refined_deg 1.667 r_mcangle_it 1.564 r_mcbond_it 0.933 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.27 r_dihedral_angle_4_deg 19.738 r_dihedral_angle_3_deg 17.589 r_dihedral_angle_1_deg 5.777 r_scangle_it 2.829 r_scbond_it 1.798 r_angle_refined_deg 1.667 r_mcangle_it 1.564 r_mcbond_it 0.933 r_nbtor_refined 0.31 r_nbd_refined 0.23 r_xyhbond_nbd_refined 0.21 r_symmetry_vdw_refined 0.201 r_chiral_restr 0.112 r_symmetry_hbond_refined 0.067 r_metal_ion_refined 0.045 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1672 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement BBS data collection MOSFLM data reduction SCALA data scaling AMoRE phasing