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Crystal structure of Arabidopsis thaliana 5-enol-pyruvyl-shikimate-3-phosphate synthase (EPSPS) in open conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NVS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 292 75% of Index G12 (0.2 M Magnesium chloride hexahydrate 0.1 M HEPES pH 7.5 25% w/v Polyethylene glycol 3,350) + 10 mM glyphosate
2+2 drop
Cryoprotection: Index G12+20% ethylene glycol;
0.5 ul of 200 mM glyphosate was added to 10 ul of cryo solution
Crystal Properties Matthews coefficient Solvent content 2.41 48.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.41 α = 90 b = 108.41 β = 90 c = 156.81 γ = 90
Symmetry Space Group I 4 2 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 EIGER X 16M 2018-10-20 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 1.4 80 99.9 0.066 0.999 21.8 18.5 92087 22.24
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 1.4 1.48 99.7 1.4 0.784 2.1 18.7
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 FREE R-VALUE 3nvs 1.4 47.08 1.35 92074 1012 99.91 0.1521 0.1517 0.1517 0.1898 0.1895 31.48
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 12.6966 f_angle_d 1.013 f_chiral_restr 0.0936 f_plane_restr 0.0114 f_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3327 Nucleic Acid Atoms Solvent Atoms 478 Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement XDS data reduction PHASER phasing XDS data scaling