Experiment: 9RUO

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9RUI

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.2	293.15	The protein was crystallized at 17.6 mg/ml in 25 mM Tris-HCl pH 7.6, 10% v/v glycerol, 0.1 mM ZnCl2, and 2 mM dithiothreitol. Initial screening was performed on a 96-Well MRC 2-Drop polystyrene Crystallization Plate (SWISSCI). From the initial hit, crystallization was further refined and performed aerobically at 20 degrees Celsius using the sitting drop method on CombiClover Jr crystallization plates (Molecular Dimensions). The reservoir chamber was filled with 100 ul of the crystallization solution containing: 50 % (v/v) Polyethylene glycol 200, 100 mM Sodium Potassium phosphate pH 6.2, and 200 mM Sodium chloride. The crystallization drop was formed by spotting 0.9 ul of purified protein with 0.9 ul of precipitant. The crystal was soaked in the crystallization solution supplemented with 16% (v/v) iodomethane (CH3I) for 4.8 minutes before being frozen in liquid nitrogen

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.74

Symmetry
Space Group	C 1 2 1

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		2024-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM07	0.97951	ESRF	BM07

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	1.62	77.02	91.6	0.075	0.08	0.028	0.999	13	8		76703

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	1.62	1.79	59.8		1.41	1.504	0.514	0.456	1.4	8.4

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	MOLECULAR REPLACEMENT	FREE R-VALUE	1.62	30.92	1.33	76597	3782	66.59	0.1789	0.1778	0.1836	0.1989	0.2015	37.42

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	15.836
f_angle_d	0.908
f_chiral_restr	0.054
f_bond_d	0.007
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6638
Nucleic Acid Atoms
Solvent Atoms	469
Heterogen Atoms	299

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.

9RUO | pdb_00009ruo