6YJB

VcaM4I restriction endonuclease 5hmC-ssDNA complex

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	EMBL/DESY, HAMBURG BEAMLINE X13
Synchrotron site	EMBL/DESY, HAMBURG
Beamline	X13
Temperature [K]	100
Detector technology	PIXEL
Collection date	2019-11-28
Detector	DECTRIS EIGER X 16M
Wavelength(s)	1.0064
Spacegroup name	P 62 2 2
Unit cell lengths	128.685, 128.685, 110.895
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	29.770 - 1.550
R-factor	0.1436
Rwork	0.142
R-free	0.16360
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	6yex
RMSD bond length	0.008
RMSD bond angle	1.358
Data reduction software	XDS
Data scaling software	XDS
Phasing software	PHASER
Refinement software	REFMAC (5.8.0258)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	29.770	1.640
High resolution limit [Å]	1.550	1.550
Rmeas	0.103	2.364
Number of reflections	78576	12449
<I/σ(I)>	26.96	1.96
Completeness [%]	99.9	99.7
Redundancy	39.2	39.9
CC(1/2)	1.000	0.752

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	8.5	291	Reservoir solution: 1.6 M (NH4)2SO4, 0.1 M MES pH 5.25; protein:DNA solution: 300 mM NaCl, 15 mM Tris-HCl pH 8.5 and 1mM TCEP. For cryo-protection the reservoir solution was diluted with glycerol to achieve 30% concentration. 0.1 M spermine tetrahydrochloride was used as an additive.