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Crystal Structure of the Naphthalene 1,2-Dioxygenase F352V Mutant Bound to Anthracene.
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 2.68 54.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.457 α = 90 b = 139.457 β = 90 c = 208.219 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 1.7 16.91 99.7 0.072 11.1 5.55 85038 85038
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) 1.7 1.76 100 0.481 2.9 5.47 8437
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 1.7 16.91 84962 84962 4248 99.52 0.161 0.161 0.159 0.171 0.194 0.2071 RANDOM 19.986
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] 0.41 0.2 0.41 -0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.018 r_dihedral_angle_4_deg 17.952 r_dihedral_angle_3_deg 13.041 r_sphericity_free 8.274 r_dihedral_angle_1_deg 6.379 r_scangle_it 3.075 r_scbond_it 2.259 r_sphericity_bonded 2.185 r_rigid_bond_restr 1.714 r_mcangle_it 1.511
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.018 r_dihedral_angle_4_deg 17.952 r_dihedral_angle_3_deg 13.041 r_sphericity_free 8.274 r_dihedral_angle_1_deg 6.379 r_scangle_it 3.075 r_scbond_it 2.259 r_sphericity_bonded 2.185 r_rigid_bond_restr 1.714 r_mcangle_it 1.511 r_angle_refined_deg 1.381 r_mcbond_it 1.265 r_angle_other_deg 0.886 r_mcbond_other 0.385 r_symmetry_vdw_other 0.253 r_nbd_refined 0.209 r_nbd_other 0.206 r_symmetry_vdw_refined 0.187 r_nbtor_refined 0.18 r_symmetry_hbond_refined 0.174 r_xyhbond_nbd_refined 0.132 r_nbtor_other 0.087 r_chiral_restr 0.081 r_bond_refined_d 0.012 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 5079 Nucleic Acid Atoms Solvent Atoms 581 Heterogen Atoms 116
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction d*TREK data reduction