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Crystal Structure Analysis of the Short-Chain Dehydrogenase/Reductase GoSDR for Patulin Detoxification
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 298 3.5 M NaCl, 0.12 M Bis-Tris, pH 7.0
Crystal Properties Matthews coefficient Solvent content 5.15 76.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 186.078 α = 90 b = 186.078 β = 90 c = 166.772 γ = 120
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 2025-10-04 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.978 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.98 49.23 99.52 0.999 36.07 19.19 76904
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.98 2.03 0.999
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 1.98 49.23 73106 3798 99.52 0.17022 0.16916 0.1786 0.19075 0.2013 RANDOM 39.943
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] 0.55 0.27 0.55 -1.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.262 r_dihedral_angle_4_deg 27.686 r_dihedral_angle_3_deg 13.938 r_long_range_B_refined 8.261 r_long_range_B_other 8.256 r_scangle_other 6.928 r_dihedral_angle_1_deg 6.653 r_scbond_it 5.058 r_scbond_other 5.057 r_mcangle_it 4.404
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.262 r_dihedral_angle_4_deg 27.686 r_dihedral_angle_3_deg 13.938 r_long_range_B_refined 8.261 r_long_range_B_other 8.256 r_scangle_other 6.928 r_dihedral_angle_1_deg 6.653 r_scbond_it 5.058 r_scbond_other 5.057 r_mcangle_it 4.404 r_mcangle_other 4.404 r_mcbond_it 3.724 r_mcbond_other 3.722 r_angle_refined_deg 1.883 r_angle_other_deg 1.539 r_chiral_restr 0.091 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001 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 3782 Nucleic Acid Atoms Solvent Atoms 272 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement SAINT data scaling PDB_EXTRACT data extraction autoPX data reduction PHASER phasing