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Structure of proline utilization A co-crystallized with 4-methoxybenzyl alcohol
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 293 Reservoir contained 0.1 M HEPES, pH 7.5, 0.1 M sodium formate, 0.1 M magnesium chloride, 0.2 M ammonium sulfate, and 18% (w/v) PEG 3350. Enzyme was incubated with 20 mM 4-Methoxybenzyl alcohol. Crystal was soaked in cryobuffer containing 67 mM 4-Methoxybenzyl alcohol and 20% PEG 200
Crystal Properties Matthews coefficient Solvent content 2.36 47.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.745 α = 90 b = 101.959 β = 106.32 c = 126.167 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 EIGER2 S 9M 2023-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.000090 ALS 8.2.1
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 1.32 48.34 94.3 0.052 0.056 0.021 0.999 16.6 6.6 1056665
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 1.32 1.34 62.5 1.72 1.942 0.886 0.352 4.6
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 1.32 46.99 0.05 1056665 53398 93.3 0.1692 0.1682 0.1665 0.1878 0.1861
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 16.824 f_angle_d 0.961 f_chiral_restr 0.071 f_plane_restr 0.008 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17891 Nucleic Acid Atoms Solvent Atoms 2660 Heterogen Atoms 330
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing