Experiment: 10YN

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8SUJ

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	289	40 mM NaOAc, pH 5.5, 1M ammonium sulfate, 0.5 M lithium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.09

Symmetry
Space Group	P 1 21 1

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	neutron	293	IMAGE PLATE	MAATEL IMAGINE		2024-10-02	L	LAUE
2	1	x-ray	293	PIXEL	DECTRIS EIGER R 4M		2024-10-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	NUCLEAR REACTOR	ORNL High Flux Isotope Reactor BEAMLINE CG4D	2.8 - 4.5	ORNL High Flux Isotope Reactor	CG4D
2	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5406

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	2.4	58.8	77.3	0.183			0.101	0.957		3.8	3.5		28304
2	1.65	95.4	99.1	0.067			0.039	0.967		19.1	3.8		109873

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	2.4	2.52		0.301			0.171	0.686		2.3	3.1
2	1.65	1.71		0.361			0.251	0.823		2.5	2.4

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	2.4	40		2.5		23605	1120	65.1			0.236		0.263		random	19.89
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	1.65	29.4		2.5		98994	5014	89.3			0.189	0.3423	0.197	0.3421	random	19.89

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
x_torsion_deg	19
x_torsion_deg	19
x_torsion_impr_deg	1.12
x_torsion_impr_deg	1.12
x_angle_deg	1.1
x_angle_deg	1.1
x_bond_d	0.009
x_bond_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6250
Nucleic Acid Atoms
Solvent Atoms	505
Heterogen Atoms	10

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.

10YN | pdb_000010yn