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Structure of proline utilization A with cis-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), cis-4-hydroxy-D-proline (50 mM), and NAD+ (10 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 2.36 47.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.89 α = 90 b = 101.92 β = 106.44 c = 126.2 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 2018-05-29 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 1.46 48.382 91 0.062 0.071 0.033 0.998 12.2 3.8 385095
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 1.46 1.48 52.8 1.298 1.684 1.055 0.323 2.3
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 1.46 48.382 0.31 384465 19052 90.84 0.195 0.1937 0.1946 0.22 0.2203 23.4749
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 17922 Nucleic Acid Atoms Solvent Atoms 1998 Heterogen Atoms 240
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction PHENIX phasing