8DYK | pdb_00008dyk

Room temperature neutron structure of a fluorescent Ag8 cluster templated by a multistranded DNA scaffold

NEUTRON DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	1.5 mM A2C4, 9mM AgNO3, 70 mM cacodylate buffer (pH 6), 2-methyl-2,4-pentanediol (MPD)

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.568	α = 90
b = 33.568	β = 90
c = 63.741	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	neutron	293	AREA DETECTOR	ORNL ANGER CAMERA		2021-05-07	L	LAUE

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SPALLATION SOURCE	ORNL Spallation Neutron Source BEAMLINE MANDI	2.0-4.0	ORNL Spallation Neutron Source	MANDI

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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
1	2.1	12.26	96.49	0.146	0.1588	0.059	0.991	10.5	6.2		2315			13.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.175	95.15		0.2635	0.2901	0.1152	0.328	3.77	5.6

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-Free (Depositor)	Mean Isotropic B
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6NIZ	2.1	12.26	1.65	2315	232	97.06	0.2325	0.2263	0.2868	18.74

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	25.6992
f_angle_d	0.7952
f_chiral_restr	0.0375
f_bond_d	0.0058
f_plane_restr	0.0016

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	230
Solvent Atoms	24
Heterogen Atoms	11

Software

Software
Software Name	Purpose
PHENIX	refinement
Mantid	data reduction
LAUENORM	data scaling
PHASER	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 R01GM157729.