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CRYSTAL STRUCTURE OF THE A149T VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR FORREST IN COMPLEX WITH PLP-GLYCINE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6UXH Chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M Ammonium tartrate dibasic pH 7.0
12% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 3.05 59.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 175.306 α = 90 b = 175.306 β = 90 c = 186.332 γ = 120
Symmetry Space Group P 31 2 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 2024-10-17 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 2.25 48.86 100 0.175 0.179 0.04 0.999 20.8 20.3 156345 30.05
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 2.25 2.33 99.9 1.379 1.421 0.341 0.868 3 17.5
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 MOLECULAR REPLACEMENT FREE R-VALUE 2.25 48.86 1.05 155196 7645 99.28 0.2671 0.2648 0.2658 0.3109 0.3102 37.75
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 14.8403 f_angle_d 0.8624 f_chiral_restr 0.048 f_bond_d 0.0071 f_plane_restr 0.0068
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17182 Nucleic Acid Atoms Solvent Atoms 608 Heterogen Atoms 100
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing