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Crystal structure of 2,2',3-trihydroxybiphenyl 1,2-dioxygenase from dibenzofuran-degrading Sphingomonas wittichii strain RW1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Crystal structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase from Rhodococcus globerulus strain P6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 294 1.4-2.0 M (NH4)2SO4, 2% PEG 400 and 0.1 M PIPES at pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 1.727 28.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.587 α = 90 b = 131.587 β = 90 c = 103.146 γ = 90
Symmetry Space Group P 43 21 2
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 MAR scanner 300 mm plate 2005-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
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 2.1 92.85 98.1 0.094 0.094 14.6 7.4 53614 51572 -3 36
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 2.1 2.18 91.1 0.499 0.499 2 3 4815
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 Crystal structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase from Rhodococcus globerulus strain P6 2.1 92.85 52592 49806 2647 97.94 0.25559 0.25559 0.25378 0.2543 0.28906 0.2887 RANDOM 23.474
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] -0.27 -0.27 0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.983 r_dihedral_angle_4_deg 16.161 r_dihedral_angle_3_deg 13.838 r_dihedral_angle_1_deg 5.562 r_scangle_it 2.034 r_scbond_it 1.284 r_angle_refined_deg 1.064 r_mcangle_it 0.966 r_mcbond_it 0.565 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.983 r_dihedral_angle_4_deg 16.161 r_dihedral_angle_3_deg 13.838 r_dihedral_angle_1_deg 5.562 r_scangle_it 2.034 r_scbond_it 1.284 r_angle_refined_deg 1.064 r_mcangle_it 0.966 r_mcbond_it 0.565 r_nbtor_refined 0.3 r_symmetry_vdw_refined 0.246 r_nbd_refined 0.206 r_symmetry_hbond_refined 0.145 r_xyhbond_nbd_refined 0.126 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8952 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 52
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling