7KZG

Human MBD4 glycosylase domain bound to DNA containing oxacarbenium-ion analog 1-aza-2'-deoxyribose

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	2020-10-24
Detector	DECTRIS PILATUS 6M
Wavelength(s)	0.9795
Spacegroup name	P 21 21 21
Unit cell lengths	41.465, 56.414, 102.733
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	37.980 - 1.680
R-factor	0.1699
Rwork	0.168
R-free	0.20460
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]	37.980	37.980	1.710
High resolution limit [Å]	1.680	9.050	1.680
Rmeas	0.333	0.097	6.403
Rpim	0.091	0.030	1.723
Total number of observations	367050	2643	19077
Number of reflections	28121	230	1429
<I/σ(I)>	10.2	35.3	1.5
Completeness [%]	99.6	99.1	100
Redundancy	13.1	11.5	13.3
CC(1/2)	0.994	0.973	0.416

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	PEG1000, HEPES