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Crystal structure determination of Catechol 1,2-Dioxygenase from Rhodococcus opacus 1CP in complex with catechol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HGI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 296 39% PEG400, 0.1 M magnesium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.01 38.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.829 α = 90 b = 37.482 β = 95.73 c = 74.479 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 2007-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.000 ELETTRA 5.2R
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 1.55 44.324 99.8 0.074 11.8 3.4 33822 22.215
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) 1.55 1.63 99.9 0.551 2 2.9 14728
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 3HGI 1.55 20 33822 1779 99.63 0.21008 0.20846 0.2081 0.239 0.2398 RANDOM 27.015
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] 0.9 0.51 -0.07 -0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.13 r_dihedral_angle_4_deg 24.892 r_dihedral_angle_3_deg 14.657 r_dihedral_angle_1_deg 5.896 r_scangle_it 3.269 r_scbond_it 2.26 r_mcangle_it 1.536 r_angle_refined_deg 1.534 r_mcbond_it 0.967 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.13 r_dihedral_angle_4_deg 24.892 r_dihedral_angle_3_deg 14.657 r_dihedral_angle_1_deg 5.896 r_scangle_it 3.269 r_scbond_it 2.26 r_mcangle_it 1.536 r_angle_refined_deg 1.534 r_mcbond_it 0.967 r_nbtor_refined 0.317 r_nbd_refined 0.214 r_symmetry_hbond_refined 0.214 r_symmetry_vdw_refined 0.206 r_xyhbond_nbd_refined 0.178 r_chiral_restr 0.127 r_metal_ion_refined 0.059 r_symmetry_metal_ion_refined 0.051 r_bond_refined_d 0.013 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2002 Nucleic Acid Atoms Solvent Atoms 287 Heterogen Atoms 70
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling