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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 PH7.5, 1.0M AMMONIUM SULFATE, VAPOR DIFFUSION, pH 7.50, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.5 50.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.29 α = 90 b = 112.694 β = 90 c = 136.542 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 37.56 97.3 0.069 4.7 415716
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 87 0.329 4.1
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 37.56 394714 20896 97.1 0.105 0.104 0.1196 0.131 0.1447 RANDOM 11.8
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] 0.46 -0.04 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.924 r_dihedral_angle_4_deg 22.693 r_sphericity_free 22.337 r_dihedral_angle_3_deg 12.343 r_sphericity_bonded 7.51 r_scangle_it 6.718 r_dihedral_angle_1_deg 6.688 r_scbond_it 5.333 r_mcangle_it 3.588 r_mcbond_it 3.024
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.924 r_dihedral_angle_4_deg 22.693 r_sphericity_free 22.337 r_dihedral_angle_3_deg 12.343 r_sphericity_bonded 7.51 r_scangle_it 6.718 r_dihedral_angle_1_deg 6.688 r_scbond_it 5.333 r_mcangle_it 3.588 r_mcbond_it 3.024 r_rigid_bond_restr 2.636 r_angle_refined_deg 2.442 r_angle_other_deg 1.202 r_mcbond_other 1.02 r_symmetry_hbond_refined 0.322 r_symmetry_vdw_other 0.273 r_nbd_refined 0.262 r_symmetry_vdw_refined 0.259 r_xyhbond_nbd_refined 0.247 r_nbd_other 0.229 r_nbtor_refined 0.194 r_chiral_restr 0.153 r_nbtor_other 0.097 r_xyhbond_nbd_other 0.09 r_bond_refined_d 0.03 r_gen_planes_refined 0.015 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 2201 Heterogen Atoms 150
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling