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NAPHTHALENE 1,2-DIOXYGENASE WITH OXIDIZED RIESKE IRON SULPHUR CENTER 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 = 138.308 α = 90 b = 138.308 β = 90 c = 206.67 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 CHESS 80MM 1999-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 2.2 30 98 0.074 16 4.18 37958
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 2.2 2.25 98.6 0.363
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 2.2 30 36554 1925 99.4 0.208 0.1874 0.242 0.2205 RANDOM 22.83
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] 0.2 0.1 0.2 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.4 r_dihedral_angle_1_deg 4.19 r_scangle_it 3.639 r_scbond_it 2.295 r_angle_refined_deg 1.522 r_mcangle_it 1.493 r_mcbond_it 0.806 r_symmetry_hbond_refined 0.559 r_nbd_refined 0.227 r_symmetry_vdw_refined 0.205
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.4 r_dihedral_angle_1_deg 4.19 r_scangle_it 3.639 r_scbond_it 2.295 r_angle_refined_deg 1.522 r_mcangle_it 1.493 r_mcbond_it 0.806 r_symmetry_hbond_refined 0.559 r_nbd_refined 0.227 r_symmetry_vdw_refined 0.205 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.102 r_metal_ion_refined 0.073 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other 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_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 358 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling