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Crystal structure of serine hydroxymethyltransferase, isoform 2 from Arabidopsis thaliana (SHM2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SMW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 292 SHM2 15 mg/ml; drop 3+2 uL
90% Index (Hampton Research) F8 (0.2 M Ammonium sulfate, 0.1 M HEPES 7.5, 25% w/v Polyethylene glycol 3,350)
cryoprotection with 20% ethylene glycol in the F8 Index condition
Crystal Properties Matthews coefficient Solvent content 2.69 54.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.201 α = 90 b = 131.236 β = 90 c = 151.389 γ = 90
Symmetry Space Group P 21 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 CCD RAYONIX MX300-HS 2018-09-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0000 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.65 80 99.5 0.094 0.999 17.19 8 274997 18.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.75 97 1.14 0.65 1.85 7.3
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 6smw 1.65 53.84 1.34 274970 1237 99.48 0.158 0.1579 0.1597 0.1779 0.1788 25.7
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 13.9167 f_angle_d 1.0081 f_chiral_restr 0.0579 f_plane_restr 0.0082 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14980 Nucleic Acid Atoms Solvent Atoms 2116 Heterogen Atoms 160
Software Software Software Name Purpose PHENIX refinement XDS data reduction PHASER phasing