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Anaerobic Crystal Structure Analysis of 1,2-dihydroxynaphthalene dioxygenase from Pseudomonas sp. strain C18 complexed with 3,4-dihydroxybiphenyl
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HAN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 294 1.8M NaCl, 0.1M MgCl2, 0.1M Hepes, anaerobic crystallization, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 3.11 60.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.87 α = 90 b = 117.87 β = 90 c = 121.594 γ = 90
Symmetry Space Group I 4 2 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 CCD CUSTOM-MADE 2001-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.99 APS 19-BM
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 1.6 50 100 0.056 8.9 49031
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 1.6 99.9 0.738
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 1HAN 1.6 49.15 49031 2622 91.38 0.16059 0.15978 0.1616 0.17562 0.1773 RANDOM 14.069
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] 0.04 0.04 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.867 r_dihedral_angle_4_deg 17.273 r_dihedral_angle_3_deg 11.445 r_dihedral_angle_1_deg 5.862 r_scangle_it 2.355 r_scbond_it 1.527 r_angle_refined_deg 1.169 r_mcangle_it 0.967 r_mcbond_it 0.636 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.867 r_dihedral_angle_4_deg 17.273 r_dihedral_angle_3_deg 11.445 r_dihedral_angle_1_deg 5.862 r_scangle_it 2.355 r_scbond_it 1.527 r_angle_refined_deg 1.169 r_mcangle_it 0.967 r_mcbond_it 0.636 r_nbtor_refined 0.311 r_nbd_refined 0.192 r_symmetry_vdw_refined 0.154 r_symmetry_hbond_refined 0.135 r_xyhbond_nbd_refined 0.121 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2274 Nucleic Acid Atoms Solvent Atoms 349 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing