☰ Navigation Tabs
Crystal structure of sulfoquinovose-1-dehydrogenase from Pseudomonas Putida in complex with NAD+ (sulfo-ED pathway)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-P0DOV5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 . SQDH-NAD complex was achieved using co-crystallization, which was obtained from protein solution at 20 mg/mL in 50 mM TRIS buffer, 300 mM NaCl buffer pH 7.5 used to set up a drop containing 0.1 uL protein: 0.15 uL mother liquor, the latter comprising 0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES buffer pH 7.5, 25% v/v Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 33.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.893 α = 90 b = 57.021 β = 93.45 c = 91.609 γ = 90
Symmetry Space Group I 1 2 1
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 X 16M 2023-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 Diamond I03
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 1.9 46.95 99.6 0.095 0.104 0.041 0.995 10.2 6.3 33641
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 1.9 1.94 99.9 0.616 0.676 0.275 0.962 6.1
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 1.9 46.95 31971 1654 99.48 0.1972 0.1949 0.24208 0.2396 RANDOM 33.283
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] -1.94 2.04 0.81 0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.981 r_dihedral_angle_2_deg 10.129 r_dihedral_angle_1_deg 6.596 r_long_range_B_refined 5.884 r_scbond_it 4.076 r_mcangle_it 3.39 r_mcbond_it 2.766 r_angle_refined_deg 2.587 r_chiral_restr 0.181 r_bond_refined_d 0.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.981 r_dihedral_angle_2_deg 10.129 r_dihedral_angle_1_deg 6.596 r_long_range_B_refined 5.884 r_scbond_it 4.076 r_mcangle_it 3.39 r_mcbond_it 2.766 r_angle_refined_deg 2.587 r_chiral_restr 0.181 r_bond_refined_d 0.016 r_gen_planes_refined 0.015 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3666 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction MrBUMP phasing