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Crystal structure of L-phenylalanine oxidase from Psuedomonas sp.P501
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 7.5 293 0.1M HEPES pH7.5, 1.0M ammonium sulfate, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.5 50.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.877 α = 90 b = 113.029 β = 90 c = 136.463 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 2005-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.00000 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 1.35 34.18 99.9 0.089 5.5 339311
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 1.35 1.42 100 0.342 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2YR4 1.35 34.18 322071 17132 99.82 0.10439 0.10263 0.13769 0.1599 RANDOM 12.85
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] 0.75 -0.35 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.62 r_sphericity_free 24.119 r_dihedral_angle_4_deg 21.295 r_dihedral_angle_3_deg 11.858 r_sphericity_bonded 8.167 r_scangle_it 7.15 r_dihedral_angle_1_deg 6.744 r_scbond_it 5.765 r_mcangle_it 3.911 r_mcbond_it 3.339
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.62 r_sphericity_free 24.119 r_dihedral_angle_4_deg 21.295 r_dihedral_angle_3_deg 11.858 r_sphericity_bonded 8.167 r_scangle_it 7.15 r_dihedral_angle_1_deg 6.744 r_scbond_it 5.765 r_mcangle_it 3.911 r_mcbond_it 3.339 r_rigid_bond_restr 2.928 r_angle_refined_deg 2.475 r_angle_other_deg 1.27 r_mcbond_other 1.153 r_symmetry_hbond_refined 0.318 r_nbd_refined 0.251 r_symmetry_vdw_other 0.251 r_xyhbond_nbd_refined 0.238 r_nbd_other 0.225 r_symmetry_vdw_refined 0.202 r_nbtor_refined 0.193 r_chiral_restr 0.174 r_nbtor_other 0.097 r_xyhbond_nbd_other 0.046 r_bond_refined_d 0.031 r_gen_planes_refined 0.015 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10424 Nucleic Acid Atoms Solvent Atoms 1957 Heterogen Atoms 148
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling