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Crystal structure of Biphenyl dioxygenase variant RR41 with dibenzofuran
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 5000 MME AND PIPES PH 6.0
Crystal Properties Matthews coefficient Solvent content 2.3 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.979 α = 90 b = 278.125 β = 117.65 c = 92.956 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 MX-300 2005-07-21 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 2.1 100 93 0.08 16.02 4.5 210175 2 38.2
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 2.1 2.18 80 0.55 2 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 2XR8 2.15 138.68 186884 9876 92.94 0.20509 0.2036 0.281 0.23312 0.2987 RANDOM 42.576
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] 0.67 0.52 -0.68 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.881 r_dihedral_angle_4_deg 13.537 r_dihedral_angle_3_deg 13.239 r_dihedral_angle_1_deg 4.995 r_angle_refined_deg 0.92 r_scangle_it 0.627 r_scbond_it 0.385 r_mcangle_it 0.302 r_nbtor_refined 0.294 r_mcbond_it 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.881 r_dihedral_angle_4_deg 13.537 r_dihedral_angle_3_deg 13.239 r_dihedral_angle_1_deg 4.995 r_angle_refined_deg 0.92 r_scangle_it 0.627 r_scbond_it 0.385 r_mcangle_it 0.302 r_nbtor_refined 0.294 r_mcbond_it 0.17 r_nbd_refined 0.152 r_metal_ion_refined 0.141 r_symmetry_vdw_refined 0.13 r_symmetry_hbond_refined 0.126 r_xyhbond_nbd_refined 0.094 r_chiral_restr 0.059 r_bond_refined_d 0.006 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_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 29556 Nucleic Acid Atoms Solvent Atoms 652 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing