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Crystal Structure of Naphthalene 1,2-Dioxygenase 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 2.69 54.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.725 α = 90 b = 139.725 β = 90 c = 208.113 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 15.97 98.5 0.069 10 3.16 100884 100884
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 95.5 0.449 2.3 2.94 9731
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 15.97 100819 100819 5049 98.29 0.165 0.165 0.164 0.1758 0.198 0.2093 RANDOM 16.738
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] 0.48 0.24 0.48 -0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.222 r_dihedral_angle_4_deg 18.333 r_dihedral_angle_3_deg 13.426 r_sphericity_free 9.64 r_dihedral_angle_1_deg 6.489 r_scangle_it 3.194 r_scbond_it 2.588 r_rigid_bond_restr 2.222 r_sphericity_bonded 2.143 r_mcangle_it 1.475
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.222 r_dihedral_angle_4_deg 18.333 r_dihedral_angle_3_deg 13.426 r_sphericity_free 9.64 r_dihedral_angle_1_deg 6.489 r_scangle_it 3.194 r_scbond_it 2.588 r_rigid_bond_restr 2.222 r_sphericity_bonded 2.143 r_mcangle_it 1.475 r_angle_refined_deg 1.422 r_mcbond_it 1.262 r_angle_other_deg 0.898 r_mcbond_other 0.333 r_symmetry_vdw_other 0.242 r_nbd_other 0.212 r_nbd_refined 0.211 r_symmetry_vdw_refined 0.191 r_nbtor_refined 0.181 r_symmetry_hbond_refined 0.179 r_xyhbond_nbd_refined 0.144 r_nbtor_other 0.088 r_chiral_restr 0.083 r_metal_ion_refined 0.021 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 5088 Nucleic Acid Atoms Solvent Atoms 731 Heterogen Atoms 131
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction d*TREK data reduction