Experiment: 9KHW

A DNA-stabilized atomically precise silver nanorod with emission at 960 nm

X-RAY DIFFRACTION

Serial Crystallography (SX)

Serial Crystallography (SX)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	50 mM MOPS, 10 mM spermine, 10 mM KNO3, 10% MPD
2	VAPOR DIFFUSION, HANGING DROP	7	293	50 mM 3-(N-morpholino)propanesulfonic acid, 10 mM spermine, 10 mM Ca(NO3), 10% 2-methyl-2,4-pentanediol against a reservoir solution of 40% 2-methyl-2,4-pentanediol.

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 27.215	α = 90
b = 53.171	β = 103.67
c = 27.215	γ = 90

Symmetry
Space Group	P 1 21 1

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		2024-10-12	M	SINGLE WAVELENGTH
2	2	x-ray	100	PIXEL	DECTRIS EIGER2 S 16M		2024-10-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.9	Photon Factory	BL-5A
2	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.6199	MAX IV	BioMAX

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1		fixed target
2		fixed target

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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
2	1.3	26.4	97.1	0.111	0.13	0.993	7.25	3.6		35689

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
2	1.3	1.33			0.319	0.376	0.899

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	AB INITIO PHASING	FREE R-VALUE	1.3	16.82	1.98	35654	3521	97.16	0.1632	0.1631	0.1557	0.1642	0.1565

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	28.714
f_angle_d	1.21
f_chiral_restr	0.097
f_plane_restr	0.018
f_bond_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	646
Solvent Atoms	39
Heterogen Atoms	30

Software

Software
Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
Sir2014	phasing
AutoSol	phasing
XDS	data reduction