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NAPHTHALENE 1,2-DIOXYGENASE WITH NAPHTHALENE BOUND IN THE ACTIVE SITE.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EG9 PDB ENTRY 1EG9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 AMMONIUM SULPHATE 2M, MES 0.1M, DIOXANE 2-3%, pH 6.00
Crystal Properties Matthews coefficient Solvent content 2.56 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.67 α = 90 b = 139.67 β = 90 c = 208.109 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 ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.7 20 95.9 0.059 11.3 5.49 82025
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 97.5 0.19
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-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 1EG9 1.7 25 77908 4117 95.9 0.163 0.1747 0.187 0.1982 RANDOM 19.98
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] 0.53 0.27 0.53 -0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.971 r_dihedral_angle_1_deg 5.361 r_scangle_it 4.773 r_scbond_it 2.977 r_mcangle_it 1.982 r_angle_refined_deg 1.811 r_symmetry_vdw_refined 1.166 r_mcbond_it 1.103 r_angle_other_deg 0.847 r_symmetry_hbond_refined 0.606
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.971 r_dihedral_angle_1_deg 5.361 r_scangle_it 4.773 r_scbond_it 2.977 r_mcangle_it 1.982 r_angle_refined_deg 1.811 r_symmetry_vdw_refined 1.166 r_mcbond_it 1.103 r_angle_other_deg 0.847 r_symmetry_hbond_refined 0.606 r_xyhbond_nbd_other 0.277 r_nbd_refined 0.253 r_xyhbond_nbd_refined 0.248 r_nbtor_other 0.229 r_symmetry_vdw_other 0.213 r_nbd_other 0.21 r_chiral_restr 0.118 r_bond_refined_d 0.019 r_metal_ion_refined 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5089 Nucleic Acid Atoms Solvent Atoms 519 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling