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Crystal Structure of the Biphenyl Dioxygenase in complex with Biphenyl from Comamonas testosteroni Sp. Strain B-356
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GZY PDB ENTRY 3GZY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 298 20-15% PEG 4000, 100mM MES, 10-15% 2-PROPANOL, SODIUM CHLORIDE, pH 6.00, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.61 52.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.355 α = 90 b = 136.355 β = 90 c = 107.155 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 MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.58 50 95 0.087 0.087 9.5 2.5 94792 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.58 1.64 67.6 0.373 0.373 2.8 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3GZY 1.58 24.18 91502 4823 94.8 0.207 0.206 0.2196 0.218 0.2301 RANDOM 23.61
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] -0.85 -0.42 -0.85 1.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.853 r_dihedral_angle_3_deg 12.205 r_dihedral_angle_4_deg 7.511 r_dihedral_angle_1_deg 4.816 r_angle_refined_deg 0.871 r_scangle_it 0.362 r_nbtor_refined 0.293 r_scbond_it 0.23 r_mcangle_it 0.215 r_nbd_refined 0.146
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.853 r_dihedral_angle_3_deg 12.205 r_dihedral_angle_4_deg 7.511 r_dihedral_angle_1_deg 4.816 r_angle_refined_deg 0.871 r_scangle_it 0.362 r_nbtor_refined 0.293 r_scbond_it 0.23 r_mcangle_it 0.215 r_nbd_refined 0.146 r_mcbond_it 0.122 r_symmetry_vdw_refined 0.119 r_symmetry_hbond_refined 0.071 r_chiral_restr 0.059 r_xyhbond_nbd_refined 0.056 r_metal_ion_refined 0.025 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5023 Nucleic Acid Atoms Solvent Atoms 640 Heterogen Atoms 41
Software Software Software Name Purpose AMoRE phasing REFMAC refinement MAR345 data collection SCALEPACK data scaling