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Structure of the plant immune signaling node EDS1 (enhanced disease susceptibility 1) in complex with nanobody ENB73
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NFU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 Reservoir composition: 17.5 % (w/v) PEG3350, 0.2 M sodium citrate, 0.1 M Bis-Tris buffer, pH 8.5; Protein stock solution: 2.8 mg/ml protein in 50 mM sodium chloride, 1 % (v/v) glycerole, 1mM DTT, 50 mM HEPES, pH 8.0; drop composition: 1 mikroliter protein stock solution + 1 mikroliter reservoir solution; crystals were cryoprotected in 17.5 % (w/v) PEG3350, 20 % (v/v) ethylene glycol, 0.2 M sodium citrate, 0.1 M Bis-Tris buffer, pH 8.5.
Crystal Properties Matthews coefficient Solvent content 3.13 60.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.504 α = 90 b = 68.232 β = 123.44 c = 105.273 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 EIGER X 4M 2018-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.967700 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 2.344 83.773 71.1 0.117 0.117 8 3.6 31550
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.344 2.565 15.1 0.87 0.87 1.5 3.7
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 4NFU 2.344 52.57 1.35 31537 1295 71.1 0.195 0.194 0.196 0.222 0.2248
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 15.396 f_angle_d 0.522 f_chiral_restr 0.04 f_plane_restr 0.004 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5980 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing Coot model building autoPROC data reduction autoPROC data scaling STARANISO data scaling