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Structure of the P130R single variant of serine hydroxymethyltransferase 8 from Glycine max cultivar Essex complexed with PLP and glycine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UXI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.8 - 0.25 M trimethylamine N-oxide, 0.1 M Tris (pH 8.5), 21-23% (w/v) PEG MME 2000
Crystal Properties Matthews coefficient Solvent content 2.19 43.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.851 α = 90 b = 126.036 β = 90 c = 129.606 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 PILATUS 6M 2019-08-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-ID-B 0.979180 APS 14-ID-B
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 2.24 126.04 100 0.129 0.139 0.052 0.996 9.1 7.2 44709 56.93
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 2.24 2.31 100 2.42 2.603 0.954 0.996 0.9 7.2
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 FREE R-VALUE 1uxi 2.24 63.02 0.31 44709 2285 99.69 0.206 0.2037 0.2035 0.248 0.2476 64.76
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 7.9689 f_angle_d 0.9461 f_chiral_restr 0.0509 f_plane_restr 0.0074 f_bond_d 0.0072
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6998 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 44
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing