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Crystal structure of the WlbA (WbpB) dehydrogenase from Pseudomonas aeruginosa in complex with NAD at 1.5 angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3O9Z PDB ENTRY 3O9Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 298 16-22% PEG5000, 2% 1,2-ethanediol, 100 mM PIPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.39 48.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.215 α = 90 b = 129.562 β = 90 c = 145.237 γ = 90
Symmetry Space Group P 21 21 21
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 210r MIRRORS 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 1.5 50 93.5 0.063 0.063 33.8 6.2 206888
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) 1.5 1.53 87.6 0.334 0.334 2.3 3.4
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 (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 3O9Z 1.5 30 206888 206888 10383 93.1 0.204 0.201 0.197 0.244 0.2376 RANDOM 28.48
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] 0.17 -0.88 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.198 r_dihedral_angle_4_deg 20.352 r_dihedral_angle_3_deg 15.539 r_dihedral_angle_1_deg 6.864 r_scangle_it 5.29 r_scbond_it 3.592 r_mcangle_it 2.483 r_angle_refined_deg 2.079 r_mcbond_it 1.569 r_chiral_restr 0.146
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.198 r_dihedral_angle_4_deg 20.352 r_dihedral_angle_3_deg 15.539 r_dihedral_angle_1_deg 6.864 r_scangle_it 5.29 r_scbond_it 3.592 r_mcangle_it 2.483 r_angle_refined_deg 2.079 r_mcbond_it 1.569 r_chiral_restr 0.146 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 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 9702 Nucleic Acid Atoms Solvent Atoms 1017 Heterogen Atoms 176
Software Software Software Name Purpose HKL-3000 data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling