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Structure of the N358Y single variant ofserine hydroxymethyltransferase 8 from Glycine max cultivar Essex complexed with PLP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6UXH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.18 - 0.25 TMAO
0.1 M Tris (ph 8.5)
21-23 (w/v) % PEG MME 2000
Crystal Properties Matthews coefficient Solvent content 2.24 45.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.967 α = 90 b = 128.599 β = 90 c = 128.629 γ = 90
Symmetry Space Group P 2 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2019-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.979180 APS 24-ID-E
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 1.89 128.63 99.9 0.069 0.075 0.027 0.999 17 7.4 75185 44.98
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.89 1.93 99.9 4.323 1.678 0.339 0.5 7.6
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 MOLECULAR REPLACEMENT FREE R-VALUE 6uxh 1.89 64.31 0.31 74026 3673 98.48 0.1822 0.1803 0.1832 0.2177 0.2226 51.4
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 6.806 f_angle_d 1.0399 f_chiral_restr 0.0559 f_bond_d 0.008 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7167 Nucleic Acid Atoms Solvent Atoms 376 Heterogen Atoms 4
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing