Experiment: 8F40

Engineering Crystals with Tunable Symmetries from 14- or 16-Base-Long DNA Strands

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	Other		ideal B type DNA duplexes generated in Cadnano

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		295	30 uM 0.005 M magnesium sulfate hydrate, 0.005 M HEPES sodium pH 7.0, 0.16 M lithium sulfate monohydrate, 6 % MPD at pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
3.64	66.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.785	α = 90
b = 36.785	β = 90
c = 103.334	γ = 90

Symmetry
Space Group	P 43 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	DECTRIS EIGER X 16M		2022-11-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.03	APS	23-ID-B

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	2.45	36.78	87.2	1	14.1	10.5		2497

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	2.45	2.94			0.951		10.7

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	ideal B type DNA duplexes generated in Cadnano	2.45	36.78	1.34	2497	125	49.93	0.2266	0.2243	0.2401	0.2638	0.2718	35.57

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	37.1926
f_angle_d	1.423
f_chiral_restr	0.0619
f_bond_d	0.0117
f_plane_restr	0.0079

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	325
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
STARANISO	data scaling
PHASER	phasing