8BSB

Vc1313-LBD bound to D-lysine

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	ESRF BEAMLINE ID30B
Synchrotron site	ESRF
Beamline	ID30B
Temperature [K]	100
Detector technology	PIXEL
Collection date	2021-06-18
Detector	DECTRIS PILATUS3 6M
Wavelength(s)	0.9763
Spacegroup name	P 1
Unit cell lengths	38.337, 44.927, 56.939
Unit cell angles	75.32, 79.17, 73.69

Refinement procedure

Resolution	36.500 - 1.900
R-factor	0.1895
Rwork	0.189
R-free	0.23280
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	Vc1313-LBD with D-arg
RMSD bond length	0.003
RMSD bond angle	0.532
Data reduction software	XDS
Data scaling software	XDS
Phasing software	PHENIX (1.20rc3_4406)
Refinement software	PHENIX (1.20rc3_4406)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	36.500	1.968
High resolution limit [Å]	1.900	1.900
Rmerge	0.095	0.882
Number of reflections	26736	2676
<I/σ(I)>	7.1
Completeness [%]	96.9
Redundancy	3.4
CC(1/2)	0.995	0.612

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	8.6	293	0.1 M Tris (base) bicine pH 8.2 - 8.8, 17 - 21% v/v PEG 500 MME, 8 - 10% w/v PEG 20000. Before setting up the drops 13 mg ml-1 Vc1313-LBD was mixed with 10 mM D-lysine from a 200 mM stock. The protein-ligand mixture was then mixed with reservoir solution in a 3:1 ratio. Before flash freezing the crystal in liquid nitrogen, the PEG concentrations were raised to 23% v/v PEG 500*MME, 12% w/v PEG 20000.