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Structure of the plant immune signaling node EDS1 (enhanced disease susceptibility 1) in complex with nanobody ENB21
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 CRYSTALLIZATION CONDITIONS: RESERVOIR COMPOSITION (CONDITION A11 of MORPHEUS SCREEN):
20.0 % (V/V) GLYCEROL, 10.0 % (W/V) PEG 4000, 0.03 M MAGNESIUM CHLORIDE, 0.03 M CALCIUM CHLORIDE, 0.0609 M TRIS-BASE, 0.0391 M BICINE, PH 8.5;
PROTEIN STOCK SOLUTION: 4.1 MG/ML PROTEIN, 50 MM SODIUM CHLORIDE, 1 % (V/V) GLYCEROL, 1 MM DTT, 50 MM HEPES, PH 8.0;
DROP COMPOSITION: 150 NL PROTEIN STOCK SOLUTION PLUS 150 NL RESERVOIR SOLUTION;
CRYO CONDITIONS: THE CRYSTALS WERE FLASH FROZEN DIRECTLY FROM THE EQUILIBRATED CRYSTALLIZATION DROPS.
Crystal Properties Matthews coefficient Solvent content 3.42 64.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.192 α = 90 b = 142.192 β = 90 c = 97.802 γ = 120
Symmetry Space Group P 3 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 PILATUS 6M 2017-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.976254 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 3.473 76.586 90.8 0.182 0.182 0.187 0.043 0.993 12.1 19.5 12634
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.473 3.646 57.1 0.354 20.1
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 3.476 61.571 1.34 12593 766 83.75 0.2214 0.2185 0.2211 0.268 0.2739
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 10.87 f_angle_d 0.765 f_chiral_restr 0.051 f_plane_restr 0.006 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5880 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction autoPROC data scaling PHASER phasing