7KZ0

Human MBD4 glycosylase domain bound to DNA containing substrate analog 2'-deoxy-pseudouridine

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SSRL BEAMLINE BL9-2
Synchrotron site	SSRL
Beamline	BL9-2
Temperature [K]	100
Detector technology	PIXEL
Collection date	2020-07-02
Detector	DECTRIS PILATUS 6M
Wavelength(s)	0.9795
Spacegroup name	P 21 21 21
Unit cell lengths	41.361, 56.860, 105.416
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	38.650 - 1.570
R-factor	0.1896
Rwork	0.188
R-free	0.21510
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	4dk9
Data reduction software	XDS
Data scaling software	Aimless (0.7.4)
Phasing software	PHASER
Refinement software	PHENIX (1.17.1_3660)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	38.650	38.650	1.600
High resolution limit [Å]	1.570	8.600	1.570
Rpim	0.046	0.007	1.380
Number of reflections	35493	270	1752
<I/σ(I)>	14.1
Completeness [%]	99.8	99.5	99.7
Redundancy	26.1	23.5	24.5
CC(1/2)	0.999	1.000	0.331

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	7.4	293	PEG3350, potassium sodium tartrate