6Q6Z | pdb_00006q6z

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)
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	0.22	0.268	0.27

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.