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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 2.51 50.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.648 α = 90 b = 112.624 β = 90 c = 136.609 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 IMAGE PLATE RIGAKU RAXIS V 2006-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 0.97200 SPring-8 BL45XU
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 47.62 97.8 0.085 5.3 429065
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 1.29 93.4 0.381 4.8
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 47.62 398321 21030 97.76 0.10272 0.10137 0.1011 0.12851 0.1262 RANDOM 10.843
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] 0.21 0.27 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.856 r_sphericity_free 22.952 r_dihedral_angle_4_deg 21.227 r_dihedral_angle_3_deg 11.749 r_sphericity_bonded 8.169 r_scangle_it 6.519 r_dihedral_angle_1_deg 6.494 r_scbond_it 5.206 r_mcangle_it 3.632 r_mcbond_it 3.049
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.856 r_sphericity_free 22.952 r_dihedral_angle_4_deg 21.227 r_dihedral_angle_3_deg 11.749 r_sphericity_bonded 8.169 r_scangle_it 6.519 r_dihedral_angle_1_deg 6.494 r_scbond_it 5.206 r_mcangle_it 3.632 r_mcbond_it 3.049 r_rigid_bond_restr 2.522 r_angle_refined_deg 2.355 r_angle_other_deg 1.192 r_mcbond_other 1.027 r_nbd_refined 0.259 r_symmetry_vdw_other 0.257 r_symmetry_hbond_refined 0.251 r_xyhbond_nbd_refined 0.233 r_nbd_other 0.227 r_symmetry_vdw_refined 0.224 r_nbtor_refined 0.192 r_chiral_restr 0.161 r_nbtor_other 0.099 r_bond_refined_d 0.028 r_gen_planes_refined 0.014 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other 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 2209 Heterogen Atoms 150
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing