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CRYSTAL STRUCTURE OF P4 VARIANT OF BIPHENYL DIOXYGENASE FROM BURKHOLDERIA XENOVORANS LB400 IN COMPLEX WITH 2,6 DI CHLOROBIPHENYL
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XR8 PDB ENTRY 2XR8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 PEG 8K, PIPES PH 6
Crystal Properties Matthews coefficient Solvent content 2.3 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.728 α = 90 b = 276.762 β = 117.37 c = 92.317 γ = 90
Symmetry Space Group P 1 21 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 MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID APS 22-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 2.28 125 86 0.08 18.6 4 177300 1.5 47.5
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 2.28 2.38 51.4 0.35 1.5 1.2
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 2XR8 2.29 138.68 144572 7632 87.7 0.18863 0.18571 0.1882 0.24456 0.2467 RANDOM 50.381
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] 0.36 0.16 -0.83 0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.672 r_dihedral_angle_4_deg 16.603 r_dihedral_angle_3_deg 15.209 r_dihedral_angle_1_deg 6.071 r_scangle_it 1.691 r_angle_refined_deg 1.136 r_scbond_it 1.064 r_mcangle_it 0.718 r_mcbond_it 0.413 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.672 r_dihedral_angle_4_deg 16.603 r_dihedral_angle_3_deg 15.209 r_dihedral_angle_1_deg 6.071 r_scangle_it 1.691 r_angle_refined_deg 1.136 r_scbond_it 1.064 r_mcangle_it 0.718 r_mcbond_it 0.413 r_nbtor_refined 0.301 r_nbd_refined 0.186 r_symmetry_vdw_refined 0.142 r_symmetry_hbond_refined 0.136 r_xyhbond_nbd_refined 0.134 r_metal_ion_refined 0.109 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 29538 Nucleic Acid Atoms Solvent Atoms 993 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing