9U8D

5hmC specific restriction endonuclease Escherichia coli O157:H7 PD-T4-3 in complex with 5-Hydroxymethyl-dCTP

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SSRF BEAMLINE BL19U1
Synchrotron site	SSRF
Beamline	BL19U1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2024-04-04
Detector	DECTRIS PILATUS 6M
Wavelength(s)	1
Spacegroup name	P 41
Unit cell lengths	103.621, 103.621, 126.360
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	47.937 - 3.002
R-factor	0.2288
Rwork	0.227
R-free	0.26870
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.005
RMSD bond angle	0.778
Data reduction software	HKL-3000 (7.21)
Data scaling software	HKL-3000 (7.21)
Phasing software	PHASER (2.7.0)
Refinement software	PHENIX (1.8.4_1496)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	47.937	3.050
High resolution limit [Å]	3.000	3.000
Number of reflections	26779	1331
<I/σ(I)>	15.7
Completeness [%]	100.0
Redundancy	13.9
CC(1/2)	0.995	0.576

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	6	293.15	0.1 M MES monohydrate pH 6.0, 14% w/v Polyethylene glycol 4,000