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Structure of serine hydroxymethyltransferase 8 from Glycine max cultivar Forrest complexed with PLP-Glycine
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 M trimethylamine N-oxide, 0.1 M Tris pH 8.5, 22.5% PEG MME 2000
Crystal Properties Matthews coefficient Solvent content 2.17 43.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.727 α = 90 b = 127.445 β = 90 c = 127.733 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 CMOS RDI CMOS_8M 2018-03-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.00 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 2.35 47.412 100 0.151 0.163 0.061 0.998 11.2 7.1 38807
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 2.35 2.43 100 2.231 2.421 0.933 0.48 6.7
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 THROUGHOUT 6UXH 2.35 47.412 1.35 38710 1899 99.86 0.2121 0.2105 0.2114 0.2423 0.2414 54.6018
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 6982 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 40
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing