Experiment: 9TN9

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9TN7

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	293.15	Prior to crystallisation, fresh sample was centrifuged at 13 000 g for 3 min to remove macro-aggregates and dust. The sample was crystallised in an anaerobic chamber filled with a N2/H2 (97:3%) atmosphere, at 20 degrees Celsius. The crystallisation was done in 96-Well MRC 2-Drop polystyrene plates (SWISSCI) containing 90 uL of crystallisation solution in the reservoir. 0.7 uL of enzyme at 6.5 mg/ml + 1 mM FAD was mixed with 0.7 uL of the crystallisation solution. The crystallisation solution contained 45 % w/v pentaerythritol propoxylate (5/4 PO/OH), 100 mM sodium acetate pH 4.6, and 400 mM potassium chloride. Prior to flash-freezing in liquid nitrogen, crystals were soaked in the crystallisation solution supplemented with 50 mM sodium nitrite for 5 min.

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.17

Symmetry
Space Group	I 2 2 2

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 EIGER X 16M		2024-05-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	1.03320	SOLEIL	PROXIMA 1

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	1.2	86.86	95.1	0.067	0.074	0.031	0.998	11.9	5.4		175298

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	1.205	1.326	56.9		0.938	1.074	0.513	0.47	1.6	4.2

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	1.2	42.02	1.34	175289	8740	73.2	0.117	0.1157	0.1158	0.1427	0.1429	20.51

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	15.814
f_angle_d	1.481
f_chiral_restr	0.106
f_plane_restr	0.017
f_bond_d	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4894
Nucleic Acid Atoms
Solvent Atoms	789
Heterogen Atoms	222

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.

9TN9 | pdb_00009tn9