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Crystal structure of D-apionate oxidoisomerase from Aureimonas altamirensis in complex with NAD+(H), Zn2+, Mn2+, and malonate (covalently bound form of malonate to coenzyme)
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 293 0.2 M Sodium malonate pH 7.0
20% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.29 46.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.71 α = 90 b = 75.792 β = 90 c = 104.574 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 DECTRIS PILATUS3 6M 2026-01-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.00000 SPring-8 BL45XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.29 46.63 100 0.118 0.12 0.999 17.9 26.5 143598
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.29 1.31 1.636 1.667 0.833 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE AlphaFold 1.29 46.63 1.33 143410 7065 99.94 0.1613 0.1605 0.1598 0.1724 0.1721
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.544 f_angle_d 1.255 f_chiral_restr 0.082 f_bond_d 0.011 f_plane_restr 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4079 Nucleic Acid Atoms Solvent Atoms 877 Heterogen Atoms 106
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction XDS data scaling PHASER phasing Coot model building XDS data reduction