9HGM

Structure of human DNMT2 with bound allosteric inhibitor

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	ESRF BEAMLINE ID30B
Synchrotron site	ESRF
Beamline	ID30B
Temperature [K]	100
Detector technology	PIXEL
Collection date	2023-12-03
Detector	DECTRIS EIGER2 S 9M
Wavelength(s)	0.8731
Spacegroup name	P 21 21 21
Unit cell lengths	71.201, 97.345, 125.018
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	48.670 - 2.600
R-factor	0.2019
Rwork	0.200
R-free	0.24550
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.005
RMSD bond angle	0.581
Data reduction software	XDS (20230630)
Data scaling software	Aimless (1.12.16)
Phasing software	PHASER (2.8.3)
Refinement software	PHENIX (1.21_5207)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	48.670	2.720
High resolution limit [Å]	2.600	2.600
Rpim	0.042	0.688
Number of reflections	27445	3300
<I/σ(I)>	10.6	1.2
Completeness [%]	100.0
Redundancy	9.6
CC(1/2)	0.999	0.626

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		291.2	Crystals were grown at 291 K using sitting drop vapour diffusion. Crystallization reservoir was composed of 0.2 M magnesium chloride, 0.1 M Tris pH 8.5 and 12 % PEG8000. Crystallization drops contained 300 nL reservoir solution and 300 nL concentrated protein.