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Crystal structure of catechol 1,2-dioxygenase from Rhodococcus opacus 1CP in complex with 3-methylcatechol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HGI pdb entry 3HGI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 296 39% PEG 400, 0.1 M Hepes, 0.1 M magnesium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.03 39.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.938 α = 90 b = 37.585 β = 94.96 c = 74.81 γ = 90
Symmetry Space Group C 1 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 MAR CCD 165 mm 2007-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.0 ELETTRA 5.2R
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 44.77 94 0.098 0.098 10 2.8 15870
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) 2 2.11 90.9 0.515 0.515 2.7 2.7 2208
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT pdb entry 3HGI 2 20 15046 813 93.69 0.22936 0.22685 0.27349 0.2712 RANDOM 28.939
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] 1.71 1.41 -0.45 -1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.58 r_dihedral_angle_4_deg 22.881 r_dihedral_angle_3_deg 16.504 r_dihedral_angle_1_deg 6.368 r_scangle_it 3.772 r_scbond_it 2.488 r_angle_refined_deg 1.669 r_mcangle_it 1.483 r_mcbond_it 0.852 r_chiral_restr 0.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.58 r_dihedral_angle_4_deg 22.881 r_dihedral_angle_3_deg 16.504 r_dihedral_angle_1_deg 6.368 r_scangle_it 3.772 r_scbond_it 2.488 r_angle_refined_deg 1.669 r_mcangle_it 1.483 r_mcbond_it 0.852 r_chiral_restr 0.117 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2002 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms 51
Software Software Software Name Purpose MAR345dtb data collection REFMAC refinement MOSFLM data reduction SCALA data scaling