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Crystal structure determination of Catechol 1,2-Dioxygenase from Rhodococcus opacus 1CP in complex with protocatechuate
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 PEG 400 38%, MgCl2 0.1 M, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 1.98 37.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.42 α = 90 b = 37.39 β = 96.28 c = 74.1 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 IMAGE PLATE MAR555 FLAT PANEL 2008-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.992 SOLEIL PROXIMA 1
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 1.85 73.72 99.9 0.084 11.2 3.7 20872 18.9
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) 1.85 1.95 100 0.458 3.8 3.7 3014
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 3HGI 1.85 34.4 19646 1063 99.14 0.19725 0.19403 0.1944 0.25825 0.2574 RANDOM 19.303
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] 0.54 0.49 0.71 -1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.811 r_dihedral_angle_4_deg 22.956 r_dihedral_angle_3_deg 16.391 r_dihedral_angle_1_deg 6.326 r_scangle_it 4.064 r_scbond_it 2.695 r_angle_refined_deg 1.716 r_mcangle_it 1.696 r_mcbond_it 1.081 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.811 r_dihedral_angle_4_deg 22.956 r_dihedral_angle_3_deg 16.391 r_dihedral_angle_1_deg 6.326 r_scangle_it 4.064 r_scbond_it 2.695 r_angle_refined_deg 1.716 r_mcangle_it 1.696 r_mcbond_it 1.081 r_nbtor_refined 0.313 r_symmetry_hbond_refined 0.276 r_symmetry_vdw_refined 0.251 r_nbd_refined 0.225 r_xyhbond_nbd_refined 0.19 r_chiral_restr 0.148 r_metal_ion_refined 0.082 r_bond_refined_d 0.019 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2002 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 53
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement XDS data reduction XDS data scaling