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Vanillyl alcohol oxidase from Novosphingobium sp in complex with vanillyl alcohol
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 VAPOR DIFFUSION, SITTING DROP 293.15 Morpheus H2
Crystal Properties Matthews coefficient Solvent content 2.57 52.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.845 α = 90 b = 96.766 β = 90 c = 129.111 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 2023-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.999870 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 1.7 129.11 99.7 0.162 0.167 0.037 0.999 10.1 20 125029
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 1.7 1.73 99.7 2.466 2.535 0.584 0.707 18.6
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 1.7 90.85 118543 6198 99.48 0.22426 0.22274 0.2332 0.2535 0.2642 RANDOM 25.38
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] -0.14 -1.62 1.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.694 r_dihedral_angle_4_deg 19.286 r_dihedral_angle_3_deg 13.56 r_dihedral_angle_1_deg 7.072 r_long_range_B_refined 6.027 r_long_range_B_other 6 r_scangle_other 4.693 r_mcangle_it 3.25 r_mcangle_other 3.25 r_scbond_it 3.212
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.694 r_dihedral_angle_4_deg 19.286 r_dihedral_angle_3_deg 13.56 r_dihedral_angle_1_deg 7.072 r_long_range_B_refined 6.027 r_long_range_B_other 6 r_scangle_other 4.693 r_mcangle_it 3.25 r_mcangle_other 3.25 r_scbond_it 3.212 r_scbond_other 3.212 r_mcbond_it 2.329 r_mcbond_other 2.329 r_angle_refined_deg 1.735 r_angle_other_deg 1.449 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 7758 Nucleic Acid Atoms Solvent Atoms 558 Heterogen Atoms 146
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing