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Crystal structure of aryl-alcohol oxidase from Pleurotus eryngii in complex with p-anisic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FIM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 292 0.1 M sodium acetate, pH 4.5 and 1.0 M di-ammonium hydrogen phosphate
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 179.326 α = 90 b = 179.326 β = 90 c = 160.177 γ = 120
Symmetry Space Group P 64 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2013-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96862 Diamond I24
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 2.3 43.99 100 0.133 28.1 40.1 67615
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.42 100
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 3fim 2.3 42.3 62672 4896 99.97 0.17583 0.17431 0.1749 0.19496 0.1952 RANDOM 32.931
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] -0.63 -0.32 -0.63 2.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.779 r_dihedral_angle_4_deg 18.977 r_dihedral_angle_3_deg 13.977 r_dihedral_angle_1_deg 6.555 r_long_range_B_refined 5.866 r_mcangle_it 3.013 r_scbond_it 2.532 r_mcbond_it 1.908 r_angle_refined_deg 1.661 r_chiral_restr 0.113
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.779 r_dihedral_angle_4_deg 18.977 r_dihedral_angle_3_deg 13.977 r_dihedral_angle_1_deg 6.555 r_long_range_B_refined 5.866 r_mcangle_it 3.013 r_scbond_it 2.532 r_mcbond_it 1.908 r_angle_refined_deg 1.661 r_chiral_restr 0.113 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4298 Nucleic Acid Atoms Solvent Atoms 280 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling