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Crystal structure of the WlbA dehydrogenase from Bordetella pertussis in complex with NADH and UDP-GlcNAcA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3Q2I PDB entry 3Q2I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 295 14-18% PEG5000, 200 mM NaCl, 100 mM HEPPS, 10 mM UDP-GlcNAcA, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.25 45.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.261 α = 90 b = 319.975 β = 119.07 c = 103.8 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 ADSC QUANTUM 210 2009-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.13 30 92.7 0.061 0.061 27.8 3.8 297970 297970
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.13 2.17 75.5 0.161 0.161 3.9 2.3 12098
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3Q2I 2.13 30 297970 297970 15037 92.62 0.18714 0.18714 0.18278 0.1841 0.26913 0.2653 RANDOM 40.972
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] 2.65 1.48 -0.76 -0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.935 r_dihedral_angle_4_deg 19.682 r_dihedral_angle_3_deg 19.18 r_dihedral_angle_1_deg 7.203 r_scangle_it 5.505 r_scbond_it 3.585 r_angle_refined_deg 2.326 r_mcangle_it 1.993 r_mcbond_it 1.177 r_chiral_restr 0.145
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.935 r_dihedral_angle_4_deg 19.682 r_dihedral_angle_3_deg 19.18 r_dihedral_angle_1_deg 7.203 r_scangle_it 5.505 r_scbond_it 3.585 r_angle_refined_deg 2.326 r_mcangle_it 1.993 r_mcbond_it 1.177 r_chiral_restr 0.145 r_gen_planes_refined 0.01 r_bond_refined_d 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 41989 Nucleic Acid Atoms Solvent Atoms 617 Heterogen Atoms 1344
Software Software Software Name Purpose HKL-3000 data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling