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Crystal Structure of Naphthalene 1,2-Dioxygenase Bound to 3-Nitrotoluene.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O7H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 279.15 1.9-2.2 M Ammonium Sulfate, 4-6% Dioxane, 0.1 M MES, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 279.15K
Crystal Properties Matthews coefficient Solvent content 2.71 54.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.211 α = 90 b = 140.211 β = 90 c = 208.271 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 NOIR-1 2004-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.04021 ALS 4.2.2
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 1.6 15.95 99.2 0.1 11.8 7.07 102411 102411
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) 1.6 1.66 96.6 0.43 2.1 2.62 9895
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 RIGID BODY REFINEMENT THROUGHOUT 1O7H 1.6 15.95 102382 102382 5122 99.07 0.162 0.162 0.161 0.1755 0.197 0.2097 RANDOM 17.437
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] 0.45 0.23 0.45 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.718 r_dihedral_angle_4_deg 17.552 r_dihedral_angle_3_deg 12.584 r_sphericity_free 8.304 r_dihedral_angle_1_deg 6.454 r_scangle_it 3.095 r_scbond_it 2.284 r_sphericity_bonded 1.953 r_rigid_bond_restr 1.648 r_angle_refined_deg 1.377
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.718 r_dihedral_angle_4_deg 17.552 r_dihedral_angle_3_deg 12.584 r_sphericity_free 8.304 r_dihedral_angle_1_deg 6.454 r_scangle_it 3.095 r_scbond_it 2.284 r_sphericity_bonded 1.953 r_rigid_bond_restr 1.648 r_angle_refined_deg 1.377 r_mcangle_it 1.369 r_mcbond_it 1.162 r_angle_other_deg 0.98 r_mcbond_other 0.333 r_symmetry_vdw_other 0.243 r_nbd_refined 0.209 r_nbd_other 0.204 r_symmetry_vdw_refined 0.188 r_nbtor_refined 0.179 r_metal_ion_refined 0.167 r_xyhbond_nbd_refined 0.15 r_symmetry_hbond_refined 0.121 r_chiral_restr 0.112 r_nbtor_other 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5089 Nucleic Acid Atoms Solvent Atoms 716 Heterogen Atoms 113
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction d*TREK data reduction