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Proline utilization A complexed with the substrate L-glutamate gamma-semialdehyde 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, 14% (W/V) PEG-3350, 0.2M AMMONIUM SULFATE, 0.1M MGCL2, 0.1M HEPES AT PH 8.0, 0.1M NA FORMATE, 10 mM NAD+. CRYTAL WAS SOAKED IN 20% (W/V) PEG-200, 40 mM L-PROLINE, 1 mM COENZYME Q1, 1mM NAD+ for 1 MIN AND THEN FLASH-COOLED IN LIQUID NITROGEN
Crystal Properties Matthews coefficient Solvent content 2.35 47.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.87 α = 90 b = 101.82 β = 106.53 c = 126.03 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 CMOS RDI CMOS_8M 2022-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.07216 ALS 4.2.2
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 1.47 48.35 97.7 0.069 0.076 0.031 0.998 12.6 4.9 751867
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 1.47 1.5 78.6 0.91 1.171 0.723 0.357 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FOURIER SYNTHESIS FREE R-VALUE 1.47 48.35 0.93 751867 37444 91.9 0.1815 0.1802 0.1787 0.2068 0.2053
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 17.698 f_angle_d 1.072 f_chiral_restr 0.069 f_plane_restr 0.01 f_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17738 Nucleic Acid Atoms Solvent Atoms 1734 Heterogen Atoms 278
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHENIX phasing