Experiment: 8G4G

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	Other		7 bp ideal B type DNA duplex generated in Cadnano

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		295	4 uL 0.5 ug/uL DNA motif in 0.2* TAE/Mg2+ buffer (annealing from 95-22 degree C in 2 hours) + 5 uL crystallization buffer [2 mM magnesium chloride hexahydrate, 4 mM sodium cacodylate trihydrate, pH 5.5, 4% v/v MPD, 0.2 mM hexammine cobalt (III) chloride]

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.88

Symmetry
Space Group	H 3 2

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++		2021-12-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH2R	1.54178

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	2.17	46.43	83.9	1	15.8	13.4		2537

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	2.17	2.4			0.466	1.4

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	7 bp ideal B type DNA duplex generated in Cadnano	2.17	31.15	1.36	2527	126	67.98	0.2512	0.2508	0.25	0.2608	0.25	31.19

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	34.5833
f_angle_d	0.7931
f_chiral_restr	0.0578
f_bond_d	0.0071
f_plane_restr	0.0056

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	483
Solvent Atoms
Heterogen Atoms

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.

8G4G | pdb_00008g4g