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Crystal Structure of 4-Chlorocatechol Dioxygenase from Rhodococcus opacus 1CP in complex with protocatechuate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S9A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 9 296 ammonium sulphate, NaCl, TRIS, pH 9.0, vapor diffusion, temperature 296K
Crystal Properties Matthews coefficient Solvent content 3.53 65.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.31 α = 90 b = 87.31 β = 90 c = 185.921 γ = 120
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 MARMOSAIC 225 mm CCD 2008-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 0.979 EMBL/DESY, HAMBURG X12
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 2.35 92.96 100 0.121 0.121 14.4 6.2 33380 33380 40.53
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 2.35 2.48 100 0.504 0.504 1.2 6.1 4866
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 1S9A 2.35 30 33340 1689 99.99 0.1688 0.1663 0.1673 0.2156 0.2118 RANDOM 42.1042
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] 0.83 0.42 0.83 -1.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.25 r_dihedral_angle_4_deg 22.189 r_dihedral_angle_3_deg 15.044 r_dihedral_angle_1_deg 9.75 r_scangle_it 4.023 r_scbond_it 2.474 r_mcangle_it 1.695 r_angle_refined_deg 1.63 r_mcbond_it 0.898 r_chiral_restr 0.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.25 r_dihedral_angle_4_deg 22.189 r_dihedral_angle_3_deg 15.044 r_dihedral_angle_1_deg 9.75 r_scangle_it 4.023 r_scbond_it 2.474 r_mcangle_it 1.695 r_angle_refined_deg 1.63 r_mcbond_it 0.898 r_chiral_restr 0.109 r_bond_refined_d 0.017 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4062 Nucleic Acid Atoms Solvent Atoms 337 Heterogen Atoms 122
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection MOLREP phasing