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Crystal Structure of the Naphthalene 1,2-Dioxygenase Phe-352-Val Mutant.
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, VAPOR DIFFUSION, HANGING DROP, temperature 279.15K
Crystal Properties Matthews coefficient Solvent content 2.7 54.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.894 α = 90 b = 139.894 β = 90 c = 208.58 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 1.5 15.99 99.2 0.078 9.6 4.38 123779 123779
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 1.5 1.55 94.4 0.518 2 2.88 11687
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 1.5 15.99 123709 123709 6218 99.08 0.157 0.157 0.155 0.1689 0.186 0.2001 RANDOM 15.965
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] 0.23 0.12 0.23 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.265 r_dihedral_angle_4_deg 16.569 r_dihedral_angle_3_deg 12.849 r_sphericity_free 9.078 r_dihedral_angle_1_deg 6.477 r_scangle_it 3.515 r_scbond_it 2.567 r_sphericity_bonded 2.28 r_rigid_bond_restr 1.859 r_mcangle_it 1.559
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.265 r_dihedral_angle_4_deg 16.569 r_dihedral_angle_3_deg 12.849 r_sphericity_free 9.078 r_dihedral_angle_1_deg 6.477 r_scangle_it 3.515 r_scbond_it 2.567 r_sphericity_bonded 2.28 r_rigid_bond_restr 1.859 r_mcangle_it 1.559 r_angle_refined_deg 1.418 r_mcbond_it 1.334 r_angle_other_deg 0.891 r_mcbond_other 0.397 r_symmetry_vdw_other 0.244 r_nbd_refined 0.21 r_nbd_other 0.206 r_nbtor_refined 0.18 r_symmetry_hbond_refined 0.155 r_xyhbond_nbd_refined 0.153 r_symmetry_vdw_refined 0.151 r_chiral_restr 0.088 r_nbtor_other 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_metal_ion_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5069 Nucleic Acid Atoms Solvent Atoms 754 Heterogen Atoms 89
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction d*TREK data reduction