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Crystal structure determination of catechol 1,2-dioxygenase from rhodococcus opacus 1CP in complex with 4-chlorocatechol
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% PEG400, 0.1M Hepes, 0.1M magnesium chloride, pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.11 41.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.572 α = 90 b = 37.501 β = 95.03 c = 74.917 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 OXFORD ONYX CCD 2007-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION ENHANCE ULTRA 1.542
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.37 20 87.7 0.05 21.16 2.03 9161
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.37 2.4 79.5 0.197 2.57 1.37
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 3HGI 2.4 20 8752 400 88.2 0.199 0.195 0.194 0.288 0.2808 RANDOM 34.85
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] 0.69 1.16 0.81 -1.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.411 r_dihedral_angle_4_deg 25.169 r_dihedral_angle_3_deg 15.856 r_dihedral_angle_1_deg 5.907 r_scangle_it 2.067 r_scbond_it 1.277 r_angle_refined_deg 1.275 r_mcangle_it 0.954 r_mcbond_it 0.521 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.411 r_dihedral_angle_4_deg 25.169 r_dihedral_angle_3_deg 15.856 r_dihedral_angle_1_deg 5.907 r_scangle_it 2.067 r_scbond_it 1.277 r_angle_refined_deg 1.275 r_mcangle_it 0.954 r_mcbond_it 0.521 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.225 r_nbd_refined 0.2 r_symmetry_hbond_refined 0.197 r_xyhbond_nbd_refined 0.178 r_chiral_restr 0.092 r_metal_ion_refined 0.043 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 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 1991 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 51
Software Software Software Name Purpose CrysalisPro data collection REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling