8B28 | pdb_00008b28

Structure of an intron-retention variant of the plant immune signalling protein EDS1 from Vitis vinifera

X-RAY DIFFRACTION

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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	0.17	0.2059	0.21	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