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Anaerobic Crystal Structure Analysis of the 1,2-dihydroxynaphthalene dioxygenase from Pseudomonas sp. strain C18 complexes with 2,3-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 3.1 60.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.785 α = 90 b = 117.785 β = 90 c = 121.528 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 IMAGE PLATE RIGAKU RAXIS IV focusing mirror optics M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.54
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 1.9 50 91.8 0.058 4.3 26960
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 1.9 88.8 0.658
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 1.9 28.5 26959 2576 86.98 0.18225 0.17977 0.1739 0.20564 0.1997 RANDOM 25.719
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] -0.15 -0.15 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.589 r_dihedral_angle_4_deg 20.322 r_dihedral_angle_3_deg 12.63 r_dihedral_angle_1_deg 6.515 r_scangle_it 2.299 r_scbond_it 1.774 r_angle_refined_deg 1.339 r_mcangle_it 1.049 r_mcbond_it 0.666 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.589 r_dihedral_angle_4_deg 20.322 r_dihedral_angle_3_deg 12.63 r_dihedral_angle_1_deg 6.515 r_scangle_it 2.299 r_scbond_it 1.774 r_angle_refined_deg 1.339 r_mcangle_it 1.049 r_mcbond_it 0.666 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.235 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.128 r_symmetry_hbond_refined 0.128 r_chiral_restr 0.095 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 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 2360 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing