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Crystal structure of eugenol oxidase in complex with isoeugenol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VAO PDB ENTRY 2VAO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 24% PEG6000, 0.1 M TRIS/HCL PH 8.0
Crystal Properties Matthews coefficient Solvent content 2.12 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.72 α = 90 b = 96.69 β = 90 c = 179.71 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 PIXEL PILATUS 2015-08-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 1.7 85 98.7 0.12 7.5 3.9 109694
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 1.7 1.73 98 0.99 1.8 3.5
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 PDB ENTRY 2VAO 1.7 89.86 104195 5370 98.41 0.16172 0.15982 0.1705 0.19881 0.2095 RANDOM 19.35
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] 0.17 0.27 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.701 r_dihedral_angle_4_deg 19.148 r_dihedral_angle_3_deg 13.199 r_dihedral_angle_1_deg 6.512 r_long_range_B_refined 5.637 r_long_range_B_other 5.637 r_scangle_other 4.614 r_scbond_it 3.068 r_scbond_other 3.068 r_mcangle_it 2.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.701 r_dihedral_angle_4_deg 19.148 r_dihedral_angle_3_deg 13.199 r_dihedral_angle_1_deg 6.512 r_long_range_B_refined 5.637 r_long_range_B_other 5.637 r_scangle_other 4.614 r_scbond_it 3.068 r_scbond_other 3.068 r_mcangle_it 2.32 r_mcangle_other 2.319 r_angle_refined_deg 1.988 r_mcbond_it 1.681 r_mcbond_other 1.681 r_angle_other_deg 1.134 r_chiral_restr 0.127 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8245 Nucleic Acid Atoms Solvent Atoms 627 Heterogen Atoms 136
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling MOLREP phasing