Experiment: 7XDJ

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7DQ0

Crystallization

Crystalization Experiments
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%)

Crystal Properties
Matthews coefficient	Solvent content
3.28	62.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 132.522	α = 90
b = 132.522	β = 90
c = 49.595	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RAYONIX MX300HE		2018-04-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL15A1	0.91982	NSRRC	BL15A1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.4	30	99.8	0.084	0.088	0.027	13.6	11.1		24192

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.44	2.53	98.1		0.759	0.801	0.252	0.849		9.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7DQ0	2.435	24.835	1.97	24192	2436	99.51	0.2043	0.2008	0.204	0.2363	0.237	57.2815

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	596
Nucleic Acid Atoms	1156
Solvent Atoms	34
Heterogen Atoms	438

Software

Software
Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing