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Crystal structure of eugenol oxidase in complex with benzoate
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 2.11 41.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.29 α = 90 b = 96.87 β = 90 c = 179.66 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 MARRESEARCH 2015-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID13 ESRF ID13
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 1.9 89.83 99.5 0.15 8.6 4.7 79217
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 1.9 1.94 99.6 0.98 2.7 4.9
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 1.9 89.83 75252 3858 99.27 0.16722 0.16495 0.1764 0.21199 0.2218 RANDOM 22.256
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] 1.33 -0.33 -1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.817 r_dihedral_angle_4_deg 19.837 r_dihedral_angle_3_deg 13.4 r_dihedral_angle_1_deg 6.484 r_scbond_it 3.006 r_mcangle_it 2.575 r_angle_refined_deg 1.921 r_mcbond_it 1.889 r_mcbond_other 1.888 r_angle_other_deg 1.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.817 r_dihedral_angle_4_deg 19.837 r_dihedral_angle_3_deg 13.4 r_dihedral_angle_1_deg 6.484 r_scbond_it 3.006 r_mcangle_it 2.575 r_angle_refined_deg 1.921 r_mcbond_it 1.889 r_mcbond_other 1.888 r_angle_other_deg 1.098 r_chiral_restr 0.119 r_bond_refined_d 0.019 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined 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 8232 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms 154
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling MOLREP phasing