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Structure of proline utilization A with trans-4-hydroxy-D-proline bound in the L-glutamate-gamma-semialdehyde dehydrogenase active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KF6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 286 Crystallization experiments were set up with SmPutA (6 mg/mL) and trans-4-hydroxy-D-proline (50 mM) in a buffer containing 50 mM Tris (pH 8.0), 50 mM NaCl, 5% (w/v) glycerol, and 0.5 mM Tris(2-caboxyethyl)phosphine. Crystals were grown using a reservoir solution containing 19% PEG-3350, 0.2 M ammonium sulfate, 0.1 M magnesium chloride, 0.1 M HEPES (pH 8.0), and 0.1 M sodium formate. Cryobuffer: reservoir supplemented with 15 % PEG-200
Crystal Properties Matthews coefficient Solvent content 2.38 48.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.146 α = 90 b = 102.005 β = 106.45 c = 126.751 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 2018-08-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.000 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 1.41 47.03 96.5 0.06 0.071 0.038 0.998 10.7 3.4 456940
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 1.41 1.43 81.3 1.322 1.752 1.133 0.259 2.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 THROUGHOUT 5kf6 1.41 45.98 1.35 454776 22756 96.07 0.1764 0.1752 0.1847 0.1988 0.2074 22.2189
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17954 Nucleic Acid Atoms Solvent Atoms 2521 Heterogen Atoms 212
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction PHENIX phasing