6D54

Low Temperature joint X-ray/neutron structure of DNA oligonucleotide d(GTGGCCAC)2 with 2'-SeCH3 modification on Cyt5

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	303	0.1 M magnesium acetate, 30% MPD, 0.1 M MES

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.884	α = 90
b = 41.884	β = 90
c = 24.307	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	IMAGE PLATE	RIGAKU RAXIS IV++	osmic varimax	2017-12-12	M	SINGLE WAVELENGTH
2	1	neutron	100	IMAGE PLATE	LADI III	collimators	2017-11-20	L	LAUE

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54
2	NUCLEAR REACTOR	ILL BEAMLINE LADI III	2.8-4.0	ILL	LADI III

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (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	1.65	40	100	0.056						16.6	10.4		2866
2	1.9	21.3	84.6	0.179						9.1	7		1629

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.71		0.149							10.2
2	1.9	2		0.226							3.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	1.65	40		2.5	2843	2800	136	98.2			0.23	0.246	random	24.54
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	1.9	21.3		2.5	1909	1572	65	82.3			0.234	0.26	random	24.54

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
x_torsion_impr_deg	0.95
x_torsion_impr_deg	0.95
x_angle_deg	0.9
x_angle_deg	0.9
x_torsion_deg	0.7
x_torsion_deg	0.7
x_bond_d	0.006
x_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	163
Nucleic Acid Atoms
Solvent Atoms	39
Heterogen Atoms	2

Software

Software
Software Name	Purpose
nCNS	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing
LAUEGEN	data reduction
LSCALE	data scaling
CNS	phasing

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 R01GM133198.