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CRYSTAL STRUCTURE OF THE A149T VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR FORREST IN COMPLEX WITH PLP
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 Sodium acetate trihydrate pH 7.0
12% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.49 50.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 175.184 α = 90 b = 175.184 β = 90 c = 183.569 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 1.87 48.75 99.6 0.207 0.218 0.067 0.998 10.1 10.2 265645 25.83
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 1.87 1.89 97.4 2.918 3.067 0.938 0.323 10.3
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 1.87 48.75 1 264638 13252 99.23 0.219 0.2172 0.2249 0.2523 0.2593 33.94
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 14.5351 f_angle_d 0.8706 f_chiral_restr 0.0489 f_plane_restr 0.0073 f_bond_d 0.0066
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21085 Nucleic Acid Atoms Solvent Atoms 1045 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing