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Crystal Structure Analysis of the 1,2-dihydroxynaphthalene dioxygenase from Pseudomonas sp. stain C18
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HAN PDB entry 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, naerobic crystallization, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 3.11 60.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.39 α = 90 b = 118.39 β = 90 c = 120.66 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 2001-12-07 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 1.69 48.97 97.1 0.088 9.7 46344
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 1.69 97.6 0.646
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 PDB entry 1HAN 1.69 48.97 39685 2048 87.21 0.1626 0.16135 0.1618 0.18629 0.1855 RANDOM 18.756
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] 0.17 0.17 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.306 r_dihedral_angle_4_deg 21.574 r_dihedral_angle_3_deg 11.94 r_dihedral_angle_1_deg 5.861 r_scangle_it 2.62 r_scbond_it 1.836 r_angle_refined_deg 1.202 r_mcangle_it 1.099 r_mcbond_it 0.799 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.306 r_dihedral_angle_4_deg 21.574 r_dihedral_angle_3_deg 11.94 r_dihedral_angle_1_deg 5.861 r_scangle_it 2.62 r_scbond_it 1.836 r_angle_refined_deg 1.202 r_mcangle_it 1.099 r_mcbond_it 0.799 r_nbtor_refined 0.317 r_nbd_refined 0.206 r_symmetry_hbond_refined 0.202 r_symmetry_vdw_refined 0.175 r_xyhbond_nbd_refined 0.159 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2368 Nucleic Acid Atoms Solvent Atoms 267 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing