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NAPHTHALENE 1,2-DIOXYGENASE WITH NITRIC OXIDE AND INDOLE 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 2.58 52.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.6 α = 90 b = 139.6 β = 90 c = 209.303 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 1.65 25 98.3 0.06 15.8 5.1 92741
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 1.6 1.71 98 0.195 4.9
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 1.65 25 87711 4634 98.3 0.184 0.1915 0.204 0.2118 RANDOM 29.24
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] 0.47 0.23 0.47 -0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.01 r_dihedral_angle_1_deg 4.9 r_scangle_it 3.951 r_scbond_it 2.451 r_angle_refined_deg 1.7 r_mcangle_it 1.565 r_angle_other_deg 0.947 r_mcbond_it 0.861 r_symmetry_hbond_other 0.848 r_symmetry_hbond_refined 0.362
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.01 r_dihedral_angle_1_deg 4.9 r_scangle_it 3.951 r_scbond_it 2.451 r_angle_refined_deg 1.7 r_mcangle_it 1.565 r_angle_other_deg 0.947 r_mcbond_it 0.861 r_symmetry_hbond_other 0.848 r_symmetry_hbond_refined 0.362 r_xyhbond_nbd_other 0.249 r_nbd_refined 0.223 r_symmetry_vdw_refined 0.223 r_nbd_other 0.209 r_metal_ion_refined 0.206 r_symmetry_vdw_other 0.19 r_xyhbond_nbd_refined 0.186 r_chiral_restr 0.103 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_nbtor_other 0.004 r_gen_planes_other 0.003 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_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 5087 Nucleic Acid Atoms Solvent Atoms 463 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing