7XJN

Structure of VcPotD1 in complex with norspermidine

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	85.640, 87.410, 174.430
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	87.210 - 1.790
R-factor	0.185
Rwork	0.183
R-free	0.21000
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	1poy
RMSD bond length	0.010
RMSD bond angle	0.980
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]	174.428	1.793
High resolution limit [Å]	1.787	1.787
Rmeas	0.081	1.097
Rpim	0.022	0.294
Number of reflections	124265	1214
<I/σ(I)>	20.1	2.1
Completeness [%]	99.8	99.8
Redundancy	13.4	13.6
CC(1/2)	0.999	0.845

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		293	The crystal of VcPotD1 in complex with norspermidine was obtained 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 norspermidine 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).