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Crystal structure of serine hydroxymethyltransferase, isoform 4 from Arabidopsis thaliana (SHM4)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SMR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 292 D9 Index (Hampton Research);
0.1 M Tris 8.5, 25% w/v, Polyethylene glycol 3,350
cryoprotection with the reservoir condition supplemented with 20% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.26 45.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.091 α = 90 b = 130.914 β = 92.261 c = 121.778 γ = 90
Symmetry Space Group P 1 21 1
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 2018-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID
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 1.74 80 95.5 0.077 0.994 8.62 2.7 181530 23.65
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 1.74 1.84 0.592 0.645 1.99 2.6
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 6smr 1.74 49.89 1.37 181494 1088 95.49 0.1618 0.1615 0.1615 0.2014 0.2019 28.01
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 13.8277 f_angle_d 0.9798 f_chiral_restr 0.0544 f_bond_d 0.0078 f_plane_restr 0.0078
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14647 Nucleic Acid Atoms Solvent Atoms 1873 Heterogen Atoms 32
Software Software Software Name Purpose PHENIX refinement XDS data reduction PHASER phasing