7XDJ

Crystal structure of actinomycin D-echinomycin-d(AGCGCGT/ACGAGCT) complex

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	NSRRC BEAMLINE BL15A1
Synchrotron site	NSRRC
Beamline	BL15A1
Temperature [K]	100
Detector technology	CCD
Collection date	2018-04-23
Detector	RAYONIX MX300HE
Wavelength(s)	0.91982
Spacegroup name	H 3
Unit cell lengths	132.522, 132.522, 49.595
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	24.835 - 2.435
R-factor	0.2043
Rwork	0.201
R-free	0.23630
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	7dq0
Data reduction software	HKL-2000
Data scaling software	HKL-2000
Phasing software	PHENIX (1.14_3260)
Refinement software	PHENIX (1.14_3260)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	30.000	30.000	2.530
High resolution limit [Å]	2.400	5.250	2.440
Rmerge	0.084	0.058	0.759
Rmeas	0.088	0.061	0.801
Rpim	0.027	0.019	0.252
Number of reflections	24192	1205	1216
<I/σ(I)>	13.6
Completeness [%]	99.8	99.6	98.1
Redundancy	11.1	10.9	9.7
CC(1/2)		0.999	0.849

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.25 mM Oligonucleotide, 0.25 mM Echinomycin, 0.125 mM Actinomycin D, 2.5 mM Sodium cacodylate, 3.5 mM Magnesium chloride, 1 mM Spermine tetrahydrochloride, 6 mM Cobalt chloride, 1% (v/v) 2-Methyl-2,4-pentanediol, 6% (v/v) PEG 200, Reservior PEG 200 (30%)