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CRYSTAL STRUCTURE OF CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE (BPHB) FROM PANDORAEA PNOMENUSA STRAIN B-356 COMPLEX WITH CO-ENZYME NAD AND PRODUCT 2,3-DIHYDROXYBIPHENYL
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 SODIUM MALONATE, PEG3350
Crystal Properties Matthews coefficient Solvent content 2.13 42.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.394 α = 90 b = 75.394 β = 90 c = 173.567 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 CCD MARMOSAIC 225 mm CCD 2011-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 2.36 50 95 0.1 19.32 12.1 20162 2 47.592
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 2.4 69.17 99.4 0.61 2.29 7.7
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 2.4 69.17 18141 982 94.18 0.21059 0.20762 0.2082 0.26568 0.2669 RANDOM 43.265
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] 1.68 1.68 -3.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.95 r_dihedral_angle_4_deg 20.136 r_dihedral_angle_3_deg 19.538 r_dihedral_angle_1_deg 6.497 r_scangle_it 2.744 r_scbond_it 1.803 r_angle_refined_deg 1.776 r_mcangle_it 1.014 r_mcbond_it 0.619 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.95 r_dihedral_angle_4_deg 20.136 r_dihedral_angle_3_deg 19.538 r_dihedral_angle_1_deg 6.497 r_scangle_it 2.744 r_scbond_it 1.803 r_angle_refined_deg 1.776 r_mcangle_it 1.014 r_mcbond_it 0.619 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.241 r_nbd_refined 0.228 r_xyhbond_nbd_refined 0.169 r_symmetry_hbond_refined 0.163 r_chiral_restr 0.117 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 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 3978 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 102
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing