6YMG

VcaM4I restriction endonuclease in complex with 5mC-modified dsDNA

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	BESSY BEAMLINE 14.1
Synchrotron site	BESSY
Beamline	14.1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2020-01-30
Detector	DECTRIS PILATUS 6M
Wavelength(s)	0.9184
Spacegroup name	P 61 2 2
Unit cell lengths	81.111, 81.111, 617.307
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	49.100 - 3.140
R-factor	0.2428
Rwork	0.241
R-free	0.26620
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	6yex
RMSD bond length	0.003
RMSD bond angle	1.193
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]	49.100	3.330
High resolution limit [Å]	3.140	3.140
Rmeas	0.227	1.641
Number of reflections	20874	2591
<I/σ(I)>	8.6	0.89
Completeness [%]	92.8	74.4
Redundancy	9.6	5.2
CC(1/2)	0.991	0.306

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	5.25	291	Reservoir solution: 1.2 M (NH4)2SO4 , 0.1 M MES pH 5.25; protein:DNA solution: 0.3 M NaCl, 15 mM Tris-HCl pH 8.5 and 1 mM TCEP. For cryo-protection the reservoir solution was diluted with glycerol to achieve 30% concentration.