9EFA | pdb_00009efa

Chemical inhibition of the N-acetyltaurine amidohydrolase PTER reduces food intake and obesity

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289.15	200mM MgCl2, 100mM Tris pH 8.5, and 20%PEG-8k

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.877	α = 90
b = 48.403	β = 96.983
c = 83.23	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

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		2024-08-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-1	0.97946	SSRL	BL12-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim I (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	2.44	31.33	97.45	0.164	4.3	4.5		24168

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.44	6.6			0.991	0.172

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.8	31.117	16012	777	96.96	0.211	0.2073	0.2091	0.2812	0.2787	28.852

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]
0.85		-1.12	1.979		-2.481

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.176
r_dihedral_angle_6_deg	14.105
r_dihedral_angle_2_deg	8.566
r_dihedral_angle_1_deg	8.044
r_lrange_it	6.991
r_lrange_other	6.991
r_scangle_it	4.062
r_scangle_other	4.062
r_mcangle_it	4.038
r_mcangle_other	4.038
r_mcbond_it	2.382
r_mcbond_other	2.378
r_scbond_it	2.362
r_scbond_other	2.362
r_angle_refined_deg	1.597
r_angle_other_deg	0.533
r_nbd_other	0.248
r_nbd_refined	0.232
r_symmetry_nbd_other	0.212
r_nbtor_refined	0.183
r_symmetry_nbd_refined	0.183
r_xyhbond_nbd_refined	0.18
r_symmetry_xyhbond_nbd_refined	0.162
r_metal_ion_refined	0.12
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.07
r_symmetry_xyhbond_nbd_other	0.051
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5412
Nucleic Acid Atoms
Solvent Atoms	2
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
MOLREP	phasing