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Caprylic acid targets a serine hydroxymethyltransferase to kill horseweed
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SMN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 PEG 3350 , succinic acid
Crystal Properties Matthews coefficient Solvent content 2.49 50.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.868 α = 90 b = 121.868 β = 90 c = 306.401 γ = 90
Symmetry Space Group P 41 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 100 PIXEL DECTRIS PILATUS3 6M 2020-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.9792 SSRF BL17U1
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 2.86 43.12 98.01 0.193 1 17.9 17.9 53245
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.86 2.96 0.193 0.139 0.04 1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6smn 2.86 43.12 50648 2622 98.04 0.215 0.2122 0.225 0.2695 0.2729 RANDOM 78.985
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] 0.93 0.93 -1.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.903 r_dihedral_angle_3_deg 17.84 r_dihedral_angle_4_deg 15.313 r_dihedral_angle_1_deg 7.01 r_angle_refined_deg 1.382 r_angle_other_deg 1.375 r_chiral_restr 0.074 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.903 r_dihedral_angle_3_deg 17.84 r_dihedral_angle_4_deg 15.313 r_dihedral_angle_1_deg 7.01 r_angle_refined_deg 1.382 r_angle_other_deg 1.375 r_chiral_restr 0.074 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14848 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing PDB_EXTRACT data extraction