9IIB

Crystal structure of NodD-EBD (Effector Binding Domain) in complex with hesperetin from Rhizobium leguminosarum bv. vicae 3841

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SSRF BEAMLINE BL02U1
Synchrotron site	SSRF
Beamline	BL02U1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2023-03-25
Detector	DECTRIS EIGER2 S 9M
Wavelength(s)	0.97918
Spacegroup name	P 1 21 1
Unit cell lengths	50.420, 197.708, 50.468
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	35.300 - 2.750
R-factor	0.2224
Rwork	0.221
R-free	0.25230
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.011
RMSD bond angle	1.426
Data reduction software	XDS
Data scaling software	XDS
Phasing software	PHENIX
Refinement software	PHENIX ((1.20.1_4487: ???))

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	35.300	8.140	2.910
High resolution limit [Å]	2.750	5.790	2.750
Rmerge		0.030	0.341
Rmeas		0.042	0.482
Number of reflections	25640	975	2746
<I/σ(I)>	16.24
Completeness [%]	99.7
Redundancy	7
CC(1/2)	0.997	0.998	0.730

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		295	0.05 M Tris-HCl pH 7.5, 0.2 M potassium chloride, 0.05 M magnesium chloride, 10% w/v polyethylene glycol 4,000