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Proline utilization A with the covalent acyl-enzyme intermediate in the aldehyde dehydrogenase active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6X9A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 286 CRYSTALLIZATION: 5 mg/mL PROTEIN, 20% (W/V) PEG-3350, 0.15M AMMONIUM SULFATE, 0.1M MGCL2, 0.1M HEPES AT PH 8.0, 0.1M NA FORMATE, 10 mM NAD+. CRYSTAL WAS SOAKED IN 20% (W/V) PEG-200, 40 mM L-PROLINE, 1 mM COENZYME Q1, 1mM NAD+, FOR 24 HRS AND THEN FLASH-COOLED IN LIQUID NITROGEN
Crystal Properties Matthews coefficient Solvent content 2.44 49.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.779 α = 90 b = 103.119 β = 106.51 c = 127.918 γ = 90
Symmetry Space Group P 1 21 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 2021-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97918 APS 24-ID-C
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 1.74 103.12 96.2 0.161 0.187 0.094 0.986 4.5 3.8 468186
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 1.74 1.77 60.6 1.665 1.983 1.052 0.331 3
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) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 1.74 97.58 468186 22871 91.68 0.2125 0.2106 0.204 0.2491 0.2441
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 16.742 f_angle_d 1.105 f_chiral_restr 0.056 f_plane_restr 0.011 f_bond_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17632 Nucleic Acid Atoms Solvent Atoms 1141 Heterogen Atoms 247
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHENIX phasing