Experiment: 7OZZ

The crystal structure of a DNA:RNA hybrid duplex sequence CTTTTCTTTG with LNA-amide modification

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	Drop solution 0.5 mM duplex, 40 mM Sodium chloride, 6.0 mM Potassium chloride, 20 mM Sodium cacodylate trihydrate pH 7.0, 17.5% (v/v) MPD, 6.0 mM Spermine tetrahydrochloride, Well solution, Component concentrations are double the concentration of the drop solution and do not contain the oligonucleotide duplex

Crystal Properties
Matthews coefficient	Solvent content
3.32	62.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.12	α = 90
b = 54.12	β = 90
c = 48.84	γ = 120

Symmetry
Space Group	P 61

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	DECTRIS PILATUS 6M		2018-11-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.9762	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.7	27.06	99.9	0.999	23	9.7		2283

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.77			0.421

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	FREE R-VALUE	7NRP	2.7	27.06	1.35	2267	137	99.78	0.2029	0.2003	0.1976	0.2367	0.2349

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	15.35
f_angle_d	1.541
f_chiral_restr	0.067
f_bond_d	0.007
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	415
Solvent Atoms
Heterogen Atoms	1

Software

Software
Software Name	Purpose
PHENIX	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing