9SYL

Structure of human DNMT2 with bound competitive inhibitor

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	ESRF BEAMLINE MASSIF-3
Synchrotron site	ESRF
Beamline	MASSIF-3
Temperature [K]	100
Detector technology	PIXEL
Collection date	2024-12-02
Detector	DECTRIS EIGER X 4M
Wavelength(s)	0.9677
Spacegroup name	I 41
Unit cell lengths	116.165, 116.165, 70.211
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	82.140 - 1.700
R-factor	0.1584
Rwork	0.158
R-free	0.17500
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.006
RMSD bond angle	0.810
Data reduction software	XDS (20230630)
Data scaling software	Aimless (1.12.16)
Phasing software	PHASER (2.8.3)
Refinement software	PHENIX (1.21.2_5419)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	82.140	1.730
High resolution limit [Å]	1.700	1.700
Rmerge	0.122	1.894
Rpim	0.049	0.751
Number of reflections	51349	2728
<I/σ(I)>	12.2	1.5
Completeness [%]	99.8
Redundancy	14.3
CC(1/2)	0.999	0.687

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		291.15	Reservoir: 1.6 M ammonium sulfate, 0.1 M bicine pH 9 Protein at 10 mg/ml Drop composition: 250 nL reservoir and 250 nL protein sample