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X-ray crystal structures of L-phenylalanine oxidase (deaminating and decaboxylating) from Pseudomonas sp. P501. Structures of the enzyme-ligand complex and catalytic mechanism
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YR4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 297 0.1M HEPES PH 7.5, 1.0M AMMONIUM SULFATE, VAPOR DIFFUSION, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.5 50.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.269 α = 90 b = 112.843 β = 90 c = 136.49 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 210 2006-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A Photon Factory AR-NW12A
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 1.25 36.27 97.4 0.077 5 415723
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 1.25 1.32 98.4 0.347 4.9
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 2YR4 1.25 36.27 394789 20873 97 0.101 0.099 0.1152 0.128 0.14 RANDOM 10.52
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] 0.51 -0.11 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.876 r_dihedral_angle_4_deg 21.659 r_sphericity_free 20.584 r_dihedral_angle_3_deg 11.868 r_sphericity_bonded 6.962 r_dihedral_angle_1_deg 6.677 r_scangle_it 6.338 r_scbond_it 4.94 r_mcangle_it 3.356 r_mcbond_it 2.817
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.876 r_dihedral_angle_4_deg 21.659 r_sphericity_free 20.584 r_dihedral_angle_3_deg 11.868 r_sphericity_bonded 6.962 r_dihedral_angle_1_deg 6.677 r_scangle_it 6.338 r_scbond_it 4.94 r_mcangle_it 3.356 r_mcbond_it 2.817 r_rigid_bond_restr 2.37 r_angle_refined_deg 2.298 r_angle_other_deg 1.18 r_mcbond_other 0.897 r_symmetry_hbond_refined 0.31 r_nbd_refined 0.269 r_xyhbond_nbd_refined 0.238 r_symmetry_vdw_other 0.232 r_nbd_other 0.228 r_nbtor_refined 0.193 r_xyhbond_nbd_other 0.154 r_chiral_restr 0.147 r_symmetry_vdw_refined 0.128 r_nbtor_other 0.095 r_bond_refined_d 0.026 r_gen_planes_refined 0.014 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10424 Nucleic Acid Atoms Solvent Atoms 2221 Heterogen Atoms 146
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling