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Eugenol Oxidase (EUGO) from Rhodococcus jostii RHA1, mutant DTT-T425G
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FXD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.8 293 41-46% MPD and 0.1 M bis-tris propane
Crystal Properties Matthews coefficient Solvent content 2.3 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.439 α = 89.87 b = 110.197 β = 89.34 c = 117.536 γ = 68.51
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 2M 2024-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.9655 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.6 117.53 93.2 0.073 0.09 0.052 0.995 9.7 2.8 519315
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 60.1 0.906 1.132 0.669 0.42 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.6 102.75 493964 25315 93.18 0.1783 0.17728 0.188 0.19774 0.2073 RANDOM 20.927
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] -0.45 -0.02 0.36 -0.22 -0.12 0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.777 r_dihedral_angle_2_deg 8.259 r_dihedral_angle_1_deg 6.153 r_long_range_B_refined 4.899 r_long_range_B_other 4.816 r_scangle_other 3.561 r_scbond_it 2.323 r_scbond_other 2.323 r_mcangle_it 2.043 r_mcangle_other 2.043
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.777 r_dihedral_angle_2_deg 8.259 r_dihedral_angle_1_deg 6.153 r_long_range_B_refined 4.899 r_long_range_B_other 4.816 r_scangle_other 3.561 r_scbond_it 2.323 r_scbond_other 2.323 r_mcangle_it 2.043 r_mcangle_other 2.043 r_angle_refined_deg 1.604 r_mcbond_it 1.371 r_mcbond_other 1.371 r_angle_other_deg 0.554 r_chiral_restr 0.082 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 33040 Nucleic Acid Atoms Solvent Atoms 2999 Heterogen Atoms 550
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing