7XJM

Structure of VcPotD1 in complex with spermidine

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SSRF BEAMLINE BL18U1
Synchrotron site	SSRF
Beamline	BL18U1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2021-06-19
Detector	DECTRIS PILATUS 6M
Wavelength(s)	0.97915
Spacegroup name	P 21 21 21
Unit cell lengths	85.825, 87.214, 174.521
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	87.260 - 1.755
R-factor	0.184
Rwork	0.183
R-free	0.20100
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	1poy
RMSD bond length	0.010
RMSD bond angle	0.960
Data reduction software	XDS (Feb 5, 2021, built on 20210323)
Data scaling software	Aimless (version 0.5.29)
Phasing software	PHASER (2.7.17)
Refinement software	BUSTER (2.10.2)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	87.260	1.761
High resolution limit [Å]	1.755	1.755
Rmeas	0.091	1.214
Rpim	0.025	0.332
Number of reflections	131344	1255
<I/σ(I)>	16.9	2
Completeness [%]	100.0	100
Redundancy	13.4	13.2
CC(1/2)	0.999	0.779

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		293	The crystal of VcPotD1 in complex with spermidine was grown in the drop containing 1.5 ul 60 mg/ml protein (10 mM HEPES, 150 mM NaCl, pH 7.5, incubated with 32.4 mM spermidine for 2 h at 4 oC) and 1.5 ul reservoir solution (100 mM sodium cacodylate HCl/pH 6.5, 32% PEG 8000, 200 mM sodium acetate).