4LY2 | pdb_00004ly2

X-ray crystal structure of the ruthenium complex [Ru(phen)2(dppz)]2+ bound to d(TCGGTACCGA)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	Performed using the sitting drop vapour diffusion method, by adding 1ul (4mM) L-[Ru(phen)2(dppz)]2+ to a drop containing 1ul (1mM) d(TCGGTACCGA)2, and 8ul of a solution containing 12mM spermine, 10% 2-methyl-2,4-pentanediol, 40 mM sodium cacodylate pH 7.0, 80 mM NaCl and 20 mM BaCl2. This was equilibrated against 1 ml of 35% 2-methyl-2,4-pantanediol at room temperature, 20 C., VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.68	66.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.45	α = 90
b = 52.45	β = 90
c = 32.58	γ = 90

Symmetry
Space Group	P 43 21 2

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	ADSC QUANTUM 315r		2012-06-10	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	1.54980, 0.97240	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.76	52.45	98.8				4849		2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.1	37.09	2711	129	97.46	0.18968	0.18817	0.18	0.2186	0.22	RANDOM	39.17

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]
-0.6			-0.6		1.19

RMS Deviations
Key	Refinement Restraint Deviation
r_angle_other_deg	3.351
r_angle_refined_deg	3.348
r_chiral_restr	0.884
r_gen_planes_refined	0.032
r_bond_refined_d	0.016
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	202
Solvent Atoms	20
Heterogen Atoms	103

Software

Software
Software Name	Purpose
MxCuBE	data collection
SHELXS	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.