Experiment: 7JY2

Z-DNA joint X-ray/Neutron

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3QBA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	2.5 M (ND4)2SO4, 10 mM magnesium acetate, 50 mM perdeuterated 2-(N-morpholino)ethanesulfonic acid (MES)

Crystal Properties
Matthews coefficient	Solvent content
1.7	27.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 17.96	α = 90
b = 31.15	β = 90
c = 44.03	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	neutron	100	AREA DETECTOR	ORNL ANGER CAMERA		2018-10-24	L	LAUE
2	1	x-ray	100	PIXEL	Bruker PHOTON II		2019-04-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SPALLATION SOURCE	ORNL Spallation Neutron Source BEAMLINE MANDI	2.0-6.0	ORNL Spallation Neutron Source	MANDI
2	LIQUID ANODE	Excillum MetalJet D2+ 70 kV	1.3418

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	1.5	14.67	84.2					0.918		13.8	5.89		3587			5.53
2	1	18	95.9					0.999		12.8	10.5		18334			3.04

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	1.5	1.55						0.482			3.85
2	1	1.08						0.985			7.8

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	1.5	14.67				3585		84.02			0.277		0.303
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	1	18				18307	2507	95.9		0.1593	0.1563	0.1573	0.185	0.1856		25.37

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	28.5895
f_dihedral_angle_d	28.5895
f_angle_d	1.4385
f_angle_d	1.4385
f_chiral_restr	0.0768
f_chiral_restr	0.0768
f_plane_restr	0.0118
f_plane_restr	0.0118
f_bond_d	0.0116
f_bond_d	0.0116

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	240
Solvent Atoms	77
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
SAINT	data reduction
Aimless	data scaling
PHENIX	phasing

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.