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Structure of an intron-retention variant of the plant immune signalling protein EDS1 from Vitis vinifera
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6I8G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 Protein solution: 4.5 mg/ml in 300 mM sodium iodide, 1 % glycerol, 1 mM DTT, 50 mM Hepes buffer, pH 8.0).
Reservoir solution: 12 % PEG3350, 300 millimolar CsCl, 100 millimolar Bis-Tris puffer, pH 8.5.
Crystallization drop before equilibration: 1.5 mikroliter protein solution plus and 1.5 mikroliter reservoir solution.
Crystal Properties Matthews coefficient Solvent content 2.54 51.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.549 α = 90 b = 65.077 β = 105.48 c = 45.454 γ = 90
Symmetry Space Group C 1 2 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 PILATUS3 6M 2021-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.915079 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.75 43.81 71.3 0.106 0.106 0.988 5.7 2.8 29029 22.36
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.755 1.942 0.668 0.668 0.658 1.4
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 6I8G 1.75 43.81 1.34 29020 1010 71.26 0.1755 0.1744 0.1745 0.2059 0.2055 30.38
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 12.9823 f_angle_d 0.5665 f_chiral_restr 0.0425 f_plane_restr 0.0048 f_bond_d 0.0029
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2635 Nucleic Acid Atoms Solvent Atoms 266 Heterogen Atoms 32
Software Software Software Name Purpose XDS data reduction autoPROC data scaling PHENIX phasing PHENIX refinement