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Crystal Structure of Naphthalene 1,2-Dioxygenase Bound to Phenanthrene
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 2.7 54.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.947 α = 90 b = 139.947 β = 90 c = 208.464 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 QUANTUM 210 2005-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.00000 APS 17-ID
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 39.51 99.6 0.065 13.3 7.12 93678 93678
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) 1.65 1.71 100 0.306 4.5 6.63 9354
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 1.65 39.51 93388 93388 4696 99.26 0.16 0.16 0.158 0.1612 0.183 0.1861 RANDOM 17.093
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] 0.54 0.27 0.54 -0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.168 r_dihedral_angle_4_deg 16.741 r_dihedral_angle_3_deg 12.329 r_dihedral_angle_1_deg 6.229 r_sphericity_free 5.688 r_scangle_it 3.202 r_scbond_it 2.913 r_rigid_bond_restr 2.688 r_sphericity_bonded 2.284 r_mcangle_it 1.449
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.168 r_dihedral_angle_4_deg 16.741 r_dihedral_angle_3_deg 12.329 r_dihedral_angle_1_deg 6.229 r_sphericity_free 5.688 r_scangle_it 3.202 r_scbond_it 2.913 r_rigid_bond_restr 2.688 r_sphericity_bonded 2.284 r_mcangle_it 1.449 r_angle_refined_deg 1.342 r_mcbond_it 1.203 r_angle_other_deg 0.873 r_mcbond_other 0.381 r_symmetry_vdw_other 0.236 r_nbd_refined 0.212 r_nbd_other 0.203 r_nbtor_refined 0.181 r_symmetry_hbond_refined 0.169 r_symmetry_vdw_refined 0.165 r_xyhbond_nbd_refined 0.124 r_nbtor_other 0.085 r_chiral_restr 0.08 r_bond_refined_d 0.01 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 5107 Nucleic Acid Atoms Solvent Atoms 651 Heterogen Atoms 124
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction d*TREK data reduction