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Key structural role for the conserved cis-proline of soybean serine hydroxymethyltransferase
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 0.1 M Hepes, pH 7.5
20% w/v PEG 3350
2% v/v tacsimate, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.04 39.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.603 α = 90 b = 129.685 β = 90 c = 58.629 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 CMOS RDI CMOS_8M 2024-04-04 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) 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 48.57 100 0.08 0.044 0.999 13.5 7.9 43034 54.91
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 2.25 2.32 100 2.437 1.354 0.537 0.9 8.1
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 41.34 1.12 42963 2166 99.91 0.1946 0.1914 0.1933 0.2563 0.2547 68.63
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 8.2607 f_angle_d 0.9377 f_chiral_restr 0.0511 f_bond_d 0.007 f_plane_restr 0.0069
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6766 Nucleic Acid Atoms Solvent Atoms 252 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing