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Structure of proline utilization A complexed with quinoline-2-carboxylic acid
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, 0.15 M ammonium sulfate, and 22% (w/v) PEG 3350. Crystal was soaked in cryobuffer containing 50 mM quinoline-2-carboxylic acid and 20% PEG 200
Crystal Properties Matthews coefficient Solvent content 2.39 48.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.961 α = 90 b = 102.33 β = 105.96 c = 127.061 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 2023-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.072156 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 1.77 48.53 95.5 0.079 0.094 0.051 0.996 12.3 3.3 412629
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 1.77 1.8 73.2 0.917 1.192 0.749 0.426 2.3
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 1.77 48.53 412629 8529 86.58 0.1774 0.1767 0.1761 0.2129 0.2114
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 14.527 f_angle_d 0.844 f_chiral_restr 0.048 f_plane_restr 0.008 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17608 Nucleic Acid Atoms Solvent Atoms 2214 Heterogen Atoms 372
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing