6Q6Z

Structure of the plant immune signaling node EDS1 (enhanced disease susceptibility 1) in complex with nanobody ENB21


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4NFU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277.15CRYSTALLIZATION 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 coefficientSolvent content
3.4264.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 142.192α = 90
b = 142.192β = 90
c = 97.802γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-03-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.976254ESRFID23-1

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
13.47376.58690.80.1820.1820.1870.0430.99312.119.512634
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.4733.64657.10.35420.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4NFU3.47661.5711.341259376683.750.22140.21850.268
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d10.87
f_angle_d0.765
f_chiral_restr0.051
f_plane_restr0.006
f_bond_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5880
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing