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Crystal Structure of Biphenyl 2,3-Dioxygenase from Sphingomonas yanoikuyae B1 Bound to Biphenyl
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GBW PDB ENTRY 2GBW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.8 277.15 20% PEG3350, 1.0 M Sodium Chloride, 0.037M Zinc Chloride, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K, pH 6.80
Crystal Properties Matthews coefficient Solvent content 2.64 53.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.94 α = 90 b = 133.94 β = 90 c = 219.708 γ = 120
Symmetry Space Group P 31 2 1
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 4 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.8 19.481 99.4 56587 56587 47.22
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 2.8 3 98.7 0.269 6.3
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 2GBW 2.8 19.48 56587 56587 1132 100 0.238 0.237 0.2511 0.268 0.2751 30.58
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] 0.17 0.09 0.17 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.109 r_dihedral_angle_3_deg 10.618 r_dihedral_angle_4_deg 10.124 r_dihedral_angle_1_deg 4.162 r_angle_other_deg 0.698 r_angle_refined_deg 0.671 r_nbtor_refined 0.169 r_nbd_other 0.145 r_nbd_refined 0.132 r_mcangle_it 0.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.109 r_dihedral_angle_3_deg 10.618 r_dihedral_angle_4_deg 10.124 r_dihedral_angle_1_deg 4.162 r_angle_other_deg 0.698 r_angle_refined_deg 0.671 r_nbtor_refined 0.169 r_nbd_other 0.145 r_nbd_refined 0.132 r_mcangle_it 0.117 r_mcbond_it 0.113 r_symmetry_vdw_other 0.111 r_symmetry_vdw_refined 0.106 r_xyhbond_nbd_refined 0.076 r_nbtor_other 0.075 r_symmetry_hbond_refined 0.047 r_chiral_restr 0.042 r_scangle_it 0.014 r_scbond_it 0.011 r_bond_refined_d 0.005 r_mcbond_other 0.005 r_metal_ion_refined 0.002 r_bond_other_d 0.001 r_gen_planes_refined 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14987 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 60
Software Software Software Name Purpose XSCALE data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction JDirector data collection