1NOP

Crystal structure of human tyrosyl-DNA phosphodiesterase (Tdp1) in complex with vanadate, DNA and a human topoisomerase I-derived peptide

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	APS BEAMLINE 19-BM
Synchrotron site	APS
Beamline	19-BM
Temperature [K]	100
Detector technology	CCD
Collection date	2002-08-16
Detector	CUSTOM-MADE
Wavelength(s)	1.0332
Spacegroup name	P 21 21 21
Unit cell lengths	49.803, 104.719, 193.924
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	100.000 * - 2.300
R-factor	0.2083
Rwork	0.206
R-free	0.25200 *
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.014
RMSD bond angle	1.387
Data reduction software	HKL-2000
Data scaling software	SCALEPACK
Phasing software	AMoRE
Refinement software	REFMAC (5.1.24)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	95.650	2.360
High resolution limit [Å]	2.300	2.300
Rmerge	0.085 *	0.339 *
Number of reflections	41018
<I/σ(I)>		2.08
Completeness [%]	92.6 *	61.9
Redundancy	4.7

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	7.8	298	PEG 3000, sodium chloride, spermine, HEPES, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystallization Reagents

ID	crystal ID	solution ID	reagent name	concentration	details
1	1	1	PEG 3000
2	1	1	NaCl
3	1	1	spermine
4	1	1	HEPES
5	1	2	PEG 3000
6	1	2	NaCl

Crystallization Reagents in Literatures

ID	crystal ID	solution	reagent name	concentration (unit)	details
1	1	drop	Tdp1	5.5 (mg/ml)
2	1	drop	sodium orthovanadate	3 (mM)
3	1	drop	DNA	5 (mM/l)
4	1	drop	peptide	20 (mM/l)
5	1	reservoir	PEG3350	22 (%)
6	1	reservoir	HEPES	100 (mM)	pH7.8
7	1	reservoir		200 (mM)
8	1	reservoir	spermine	10 (mM)