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Crystal structure of Catechol 1,2-Dioxygenase from the gram-positive Rhodococcus opacus 1CP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BOY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 296 39% PEG400, 0.1 M Hepes, 0.1 M magnesium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.11 41.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.794 α = 90 b = 38.118 β = 94.21 c = 76.065 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 2005-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 0.949 EMBL/DESY, HAMBURG BW7A
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 1.94 22.8 98.5 0.089 0.089 11.1 3.4 19038
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) 1.94 2.05 95.6 0.264 0.264 2.6 2.4 2662
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 2BOY 1.94 20 18056 965 98.51 0.20259 0.1986 0.1987 0.27755 0.2769 RANDOM 30.67
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] 1.41 2.33 1.14 -2.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.142 r_dihedral_angle_4_deg 21.992 r_dihedral_angle_3_deg 13.408 r_dihedral_angle_1_deg 6.425 r_scangle_it 3.617 r_scbond_it 2.353 r_angle_refined_deg 1.573 r_mcangle_it 1.474 r_mcbond_it 0.874 r_chiral_restr 0.113
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.142 r_dihedral_angle_4_deg 21.992 r_dihedral_angle_3_deg 13.408 r_dihedral_angle_1_deg 6.425 r_scangle_it 3.617 r_scbond_it 2.353 r_angle_refined_deg 1.573 r_mcangle_it 1.474 r_mcbond_it 0.874 r_chiral_restr 0.113 r_bond_refined_d 0.017 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2018 Nucleic Acid Atoms Solvent Atoms 236 Heterogen Atoms 55
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling