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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, pH 7.50, VAPOR DIFFUSION, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.5 50.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.985 α = 90 b = 112.941 β = 90 c = 136.458 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 2006-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44B2 SPring-8 BL44B2
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 1.1 29.2 98.6 0.043 5.3 615937
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 1.1 1.16 97.1 0.398 5.3
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 1.1 29.2 584957 30827 98.5 0.112 0.111 0.1252 0.131 0.1432 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] 0.41 0.1 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.276 r_dihedral_angle_4_deg 22.252 r_sphericity_free 19.062 r_dihedral_angle_3_deg 11.623 r_sphericity_bonded 7.176 r_dihedral_angle_1_deg 6.525 r_scangle_it 5.854 r_scbond_it 4.628 r_mcangle_it 3.15 r_mcbond_it 2.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.276 r_dihedral_angle_4_deg 22.252 r_sphericity_free 19.062 r_dihedral_angle_3_deg 11.623 r_sphericity_bonded 7.176 r_dihedral_angle_1_deg 6.525 r_scangle_it 5.854 r_scbond_it 4.628 r_mcangle_it 3.15 r_mcbond_it 2.64 r_rigid_bond_restr 2.306 r_angle_refined_deg 2.154 r_angle_other_deg 1.141 r_mcbond_other 0.848 r_symmetry_vdw_refined 0.38 r_symmetry_hbond_refined 0.309 r_nbd_refined 0.267 r_symmetry_vdw_other 0.249 r_xyhbond_nbd_refined 0.239 r_nbd_other 0.225 r_nbtor_refined 0.191 r_chiral_restr 0.134 r_nbtor_other 0.092 r_xyhbond_nbd_other 0.037 r_bond_refined_d 0.025 r_gen_planes_refined 0.013 r_bond_other_d 0.005 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 2337 Heterogen Atoms 152
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling