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Crystal Structure of Human Catechol O-Methyltransferase with bound SAM and DNC
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H1D pdb entry 1H1D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 10.5 293 Tris, NaCl, MgCL2, DTT, CAPS, Na, K PO4, LiSO4, SAM, DNC, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.06 40.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.284 α = 90 b = 66.648 β = 90 c = 68.046 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 mirrors 2006-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54178
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 1.97 50 76.8 0.08 5.4 11145 11145 2
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) 1.97 2.04 3.3 0.448 2.3 2.3 1.1
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1H1D 1.98 33.31 11110 10559 549 78.32 0.17704 0.17465 0.22514 0.246 RANDOM 26.975
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] -1.6 1.17 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.825 r_dihedral_angle_4_deg 15.114 r_dihedral_angle_3_deg 13.331 r_dihedral_angle_1_deg 5.152 r_scangle_it 2.716 r_scbond_it 1.626 r_angle_refined_deg 1.269 r_mcangle_it 1.119 r_angle_other_deg 0.912 r_mcbond_it 0.581
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.825 r_dihedral_angle_4_deg 15.114 r_dihedral_angle_3_deg 13.331 r_dihedral_angle_1_deg 5.152 r_scangle_it 2.716 r_scbond_it 1.626 r_angle_refined_deg 1.269 r_mcangle_it 1.119 r_angle_other_deg 0.912 r_mcbond_it 0.581 r_symmetry_vdw_other 0.257 r_symmetry_hbond_refined 0.151 r_xyhbond_nbd_refined 0.128 r_mcbond_other 0.103 r_symmetry_vdw_refined 0.075 r_chiral_restr 0.067 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1695 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing