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Crystal Structure of cis-Biphenyl-2,3-dihydrodiol-2,3-dehydrogenase (BphB)from Pandoraea pnomenusa strain B-356.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BDB PDB ENTRY 1BDB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 3-5 M SODIUM FORMATE
Crystal Properties Matthews coefficient Solvent content 2 38.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.692 α = 90 b = 75.692 β = 90 c = 176.876 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2010-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR-H
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 2.2 69.5 97 0.11 13.6 5.5 26076 2 39.83
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 2.21 2.25 40.6 0.39 2.4 2.9
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 1BDB 2.22 69.5 24478 1320 98.94 0.18248 0.18054 0.1791 0.21889 0.2182 RANDOM 39.985
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] -0.23 -0.23 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.01 r_dihedral_angle_4_deg 16.113 r_dihedral_angle_3_deg 15.725 r_dihedral_angle_1_deg 5.489 r_scangle_it 1.54 r_angle_refined_deg 1.181 r_scbond_it 0.953 r_mcangle_it 0.623 r_mcbond_it 0.349 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.01 r_dihedral_angle_4_deg 16.113 r_dihedral_angle_3_deg 15.725 r_dihedral_angle_1_deg 5.489 r_scangle_it 1.54 r_angle_refined_deg 1.181 r_scbond_it 0.953 r_mcangle_it 0.623 r_mcbond_it 0.349 r_nbtor_refined 0.3 r_symmetry_hbond_refined 0.224 r_symmetry_vdw_refined 0.2 r_nbd_refined 0.187 r_xyhbond_nbd_refined 0.133 r_chiral_restr 0.083 r_bond_refined_d 0.008 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_refined 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 3926 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing