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X-ray crystal structure of the Wbpe (WlbE) aminotransferase from pseudomonas aeruginosa as the PLP internal aldimine adduct with lysine 185
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, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.16 43.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.628 α = 84.26 b = 54.068 β = 82.43 c = 150.903 γ = 64.93
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 mirrors 2009-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.99187 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 0.047 0.047 44.2 2.3 200622 200622
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 1.5 1.53 87 0.09 0.09 10.2 2 9398
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 1.501 30 200621 200621 10115 92.96 0.18287 0.18287 0.18091 0.1767 0.21945 0.2127 RANDOM 16.789
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] 0.41 0.3 -0.9 -0.17 -0.1 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.965 r_dihedral_angle_4_deg 23.159 r_dihedral_angle_3_deg 13.775 r_dihedral_angle_1_deg 6.536 r_scangle_it 5.042 r_scbond_it 3.431 r_mcangle_it 2.188 r_angle_refined_deg 1.634 r_mcbond_it 1.521 r_chiral_restr 0.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.965 r_dihedral_angle_4_deg 23.159 r_dihedral_angle_3_deg 13.775 r_dihedral_angle_1_deg 6.536 r_scangle_it 5.042 r_scbond_it 3.431 r_mcangle_it 2.188 r_angle_refined_deg 1.634 r_mcbond_it 1.521 r_chiral_restr 0.112 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 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 10950 Nucleic Acid Atoms Solvent Atoms 1489 Heterogen Atoms 22
Software Software Software Name Purpose HKL-3000 data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling