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Crystal Structure of Human 108M Catechol O-methyltransferase bound with S-adenosylmethionine and inhibitor dinitrocatechol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BWM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 Tris, NaCl, MgCL2, DTT, HEPES, MPD, SAM, DNC, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.05 40.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.249 α = 90 b = 66.163 β = 90 c = 68.519 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 MARMOSAIC 300 mm CCD 2007-08-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.910 APS 23-ID-D
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 1.3 50 82.9 0.088 10.9 4.8 40351 40351 1.6
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) 1.3 1.35 28.3 0.41 1.7 1361
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3BWM 1.3 47.62 40175 40175 2061 81.82 0.126 0.126 0.124 0.1255 0.167 0.1642 RANDOM 15.166
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] -0.87 1.61 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.086 r_dihedral_angle_4_deg 22.646 r_dihedral_angle_3_deg 12.697 r_sphericity_free 10.987 r_scangle_it 7.707 r_scbond_it 6.292 r_dihedral_angle_1_deg 5.371 r_sphericity_bonded 5.077 r_rigid_bond_restr 4.595 r_mcangle_it 4.484
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.086 r_dihedral_angle_4_deg 22.646 r_dihedral_angle_3_deg 12.697 r_sphericity_free 10.987 r_scangle_it 7.707 r_scbond_it 6.292 r_dihedral_angle_1_deg 5.371 r_sphericity_bonded 5.077 r_rigid_bond_restr 4.595 r_mcangle_it 4.484 r_mcbond_it 3.543 r_mcbond_other 2.263 r_angle_refined_deg 1.916 r_angle_other_deg 1.125 r_chiral_restr 0.134 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1715 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 42
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling