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Vanillyl alcohol oxidase from Novosphingobium sp: T181D mutant in complex with vanillin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 6.5 293.5 PEG 20000 15%, 0.1 M MES
Crystal Properties Matthews coefficient Solvent content 2.62 53.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.326 α = 90 b = 97.824 β = 90 c = 129.607 γ = 90
Symmetry Space Group P 2 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 DECTRIS EIGER R 4M 2023-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.873128 ESRF MASSIF-3
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 78.2 99.6 0.15 0.158 0.051 0.998 8.8 9.3 152440
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 99.3 1.476 1.562 0.504 0.793 9.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.6 78.2 144823 7529 99.49 0.1765 0.17512 0.20382 0.2013 RANDOM 16.011
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] -0.7 0.74 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.274 r_dihedral_angle_2_deg 7.739 r_dihedral_angle_1_deg 6.867 r_long_range_B_refined 5.68 r_long_range_B_other 5.585 r_scangle_other 4.574 r_scbond_it 3.053 r_scbond_other 3.053 r_mcangle_it 2.559 r_mcangle_other 2.559
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.274 r_dihedral_angle_2_deg 7.739 r_dihedral_angle_1_deg 6.867 r_long_range_B_refined 5.68 r_long_range_B_other 5.585 r_scangle_other 4.574 r_scbond_it 3.053 r_scbond_other 3.053 r_mcangle_it 2.559 r_mcangle_other 2.559 r_mcbond_it 1.737 r_mcbond_other 1.737 r_angle_refined_deg 1.709 r_angle_other_deg 0.579 r_chiral_restr 0.091 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 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 7740 Nucleic Acid Atoms Solvent Atoms 772 Heterogen Atoms 147
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing