6XS9

Crystal structure of human Vps29 complexed with RaPID-derived cyclic peptide RT-L1

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Synchrotron site	Australian Synchrotron
Beamline	MX2
Temperature [K]	100
Detector technology	PIXEL
Collection date	2019-05-03
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.95372
Spacegroup name	P 41 21 2
Unit cell lengths	119.440, 119.440, 125.630
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	40.692 - 2.690
R-factor	0.247789920567
Rwork	0.246
R-free	0.28184
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	1w24
RMSD bond length	0.007
RMSD bond angle	0.885
Data reduction software	XDS
Data scaling software	Aimless (0.7.3)
Phasing software	PHASER (2.5.6)
Refinement software	PHENIX (1.10.1)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	49.160	49.160	2.820
High resolution limit [Å]	2.685	8.910	2.690
Rmerge	0.092	0.043	0.648
Rmeas	0.101	0.047	0.743
Rpim	0.040	0.019	0.351
Total number of observations		4244	11469
Number of reflections	25371	731	3013
<I/σ(I)>	8.2	21	1.3
Completeness [%]	97.8	92.6	88.9
Redundancy	5.6	5.8	3.8
CC(1/2)	0.997	0.998	0.879

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	6	293	1.4 M sodium malonate