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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 ANALOG 4,4'-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 2.26 45.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.217 α = 90 b = 76.217 β = 90 c = 180.573 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 2011-04-22 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 2.15 100 99.9 0.12 19.34 8.9 30090 2 38.421
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 70.19 100 0.73 2.51 8.7
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 2.14 70.19 28211 1509 98.61 0.18845 0.18638 0.1913 0.22654 0.2332 RANDOM 40.406
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] 0.12 0.12 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.01 r_dihedral_angle_4_deg 19.361 r_dihedral_angle_3_deg 16.238 r_dihedral_angle_1_deg 6.261 r_scangle_it 2.35 r_scbond_it 1.639 r_angle_refined_deg 1.511 r_angle_other_deg 1.052 r_mcangle_it 0.904 r_mcbond_it 0.713
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.01 r_dihedral_angle_4_deg 19.361 r_dihedral_angle_3_deg 16.238 r_dihedral_angle_1_deg 6.261 r_scangle_it 2.35 r_scbond_it 1.639 r_angle_refined_deg 1.511 r_angle_other_deg 1.052 r_mcangle_it 0.904 r_mcbond_it 0.713 r_symmetry_vdw_other 0.288 r_nbd_refined 0.202 r_nbd_other 0.199 r_symmetry_vdw_refined 0.184 r_symmetry_hbond_refined 0.182 r_nbtor_refined 0.175 r_mcbond_other 0.153 r_xyhbond_nbd_refined 0.145 r_nbtor_other 0.09 r_chiral_restr 0.089 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 3976 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 102
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing