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Crystal Structure of Biphenyl dioxygenase variant RR41 (BPDO-RR41)
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 6.5
Crystal Properties Matthews coefficient Solvent content 2.3 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.969 α = 90 b = 277.808 β = 117.61 c = 92.933 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 2005-07-20 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 2.15 100 99 0.06 17.4 3.7 208106 2 37
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 2.15 2.23 94 0.38 2.2 3
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 197600 10445 99.05 0.20152 0.19992 0.2711 0.23163 0.2911 RANDOM 45.45
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] 0.56 1.12 -0.07 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.815 r_dihedral_angle_3_deg 13.329 r_dihedral_angle_4_deg 12.551 r_dihedral_angle_1_deg 5.068 r_angle_refined_deg 0.881 r_scangle_it 0.693 r_scbond_it 0.419 r_mcangle_it 0.325 r_nbtor_refined 0.294 r_mcbond_it 0.183
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.815 r_dihedral_angle_3_deg 13.329 r_dihedral_angle_4_deg 12.551 r_dihedral_angle_1_deg 5.068 r_angle_refined_deg 0.881 r_scangle_it 0.693 r_scbond_it 0.419 r_mcangle_it 0.325 r_nbtor_refined 0.294 r_mcbond_it 0.183 r_xyhbond_nbd_refined 0.168 r_nbd_refined 0.152 r_symmetry_vdw_refined 0.138 r_symmetry_hbond_refined 0.132 r_metal_ion_refined 0.085 r_chiral_restr 0.06 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 1213 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing