☰ Navigation Tabs
X-ray crystal structure of the WlbE (WpbE) aminotransferase from pseudomonas aeruginosa, mutation K185A, in complex with the PLP external aldimine adduct with UDP-3-amino-2-N-acetyl-glucuronic acid, at 1.3 angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NYS PDB ENTRY 3NYS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 25% pentaerythritol propoxylate, 100 mM MES, 50mM UDP-3-amino-20N-acetyl-glucuronic acid, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.42 49.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.684 α = 90 b = 92.17 β = 111.84 c = 75.652 γ = 90
Symmetry Space Group C 1 2 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 Bruker Platinum 135 montel 2010-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.54178
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 1.3 30 97.7 0.051 0.051 15.8 5.5 90696 90696
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 1.3 1.33 86.1 0.33 0.33 3 2.2 3399
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 3NYS 1.301 30 90693 86156 4537 97.7 0.19097 0.19097 0.18964 0.1857 0.21626 0.2103 RANDOM 14.137
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] -0.61 0.03 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.325 r_dihedral_angle_4_deg 20.342 r_dihedral_angle_3_deg 12.576 r_dihedral_angle_1_deg 6.262 r_scangle_it 5.455 r_scbond_it 3.515 r_mcangle_it 2.288 r_angle_refined_deg 2.18 r_mcbond_it 1.519 r_chiral_restr 0.146
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.325 r_dihedral_angle_4_deg 20.342 r_dihedral_angle_3_deg 12.576 r_dihedral_angle_1_deg 6.262 r_scangle_it 5.455 r_scbond_it 3.515 r_mcangle_it 2.288 r_angle_refined_deg 2.18 r_mcbond_it 1.519 r_chiral_restr 0.146 r_bond_refined_d 0.013 r_gen_planes_refined 0.013 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 2729 Nucleic Acid Atoms Solvent Atoms 470 Heterogen Atoms 56
Software Software Software Name Purpose PROTEUM PLUS data collection PHASER phasing REFMAC refinement SAINT data reduction SADABS data scaling