5CLE

Alkylpurine DNA glycosylase AlkD bound to DNA containing an abasic-site analog and a free 3-methyladenine nucleobase

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	APS BEAMLINE 21-ID-F
Synchrotron site	APS
Beamline	21-ID-F
Temperature [K]	100
Detector technology	CCD
Collection date	2014-08-02
Detector	MARMOSAIC 225 mm CCD
Wavelength(s)	0.97872
Spacegroup name	P 1 21 1
Unit cell lengths	38.492, 93.288, 48.162
Unit cell angles	90.00, 112.84, 90.00

Refinement procedure

Resolution	40.079 - 1.730
R-factor	0.1566
Rwork	0.155
R-free	0.19170
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	3bvs
RMSD bond length	0.007
RMSD bond angle	1.009
Data reduction software	HKL-2000
Data scaling software	HKL-2000
Refinement software	PHENIX

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	50.000	50.000	1.790
High resolution limit [Å]	1.730	3.730	1.730
Rmerge	0.067	0.034	0.443
Rmeas	0.074	0.038	0.500
Rpim	0.033	0.017	0.228
Total number of observations	161136
Number of reflections	32574
<I/σ(I)>	11.7		3.383
Completeness [%]	99.9	99.5	99.6
Redundancy	4.9	5	4.6
CC(1/2)		0.998	0.892

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	5.7	294	17% w/v PEG4000, 42 mM sodium acetate, pH 4.6, 85 mM ammonium acetate, 5% glycerol