Experiment: 8PIP

DNA triplex structure with Polypyridyl Ruthenium Complexes

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.16	278	A solution containing 20mM Na-cacodylate, 10mM MgCl2, 1.6mM DNA, 1.6mM rac-[Ru(phen)2(dppz)].2Cl was mixed in a 1:1 ratio with a solution containing 1.8mM LiSO4, 50mM tris-HCL pH 7.16, 1.4mM CuCl2 and 0.6mM spermine. Total drop volume was 400nL

Crystal Properties
Matthews coefficient	Solvent content
3.78	67.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.464	α = 90
b = 86.151	β = 90
c = 87.852	γ = 90

Symmetry
Space Group	I 2 2 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	PIXEL	RIGAKU HyPix-6000HE		2023-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	RIGAKU PhotonJet-S	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	20.34	99.9	0.19	0.043	0.99	15.5	40.3		9970			32.33

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.05			3.62	0.94	0.84

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	FREE R-VALUE	2	20.34	1.33	9886	925	98.71	0.2309	0.2293	0.2283	0.2585	0.2574	49.05

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	32.2544
f_angle_d	1.8142
f_chiral_restr	0.0406
f_bond_d	0.0045
f_plane_restr	0.0027

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	621
Solvent Atoms	81
Heterogen Atoms	155

Software

Software
Software Name	Purpose
PHENIX	refinement
CrysalisPro	data reduction
Aimless	data scaling
SHELXDE	phasing