9EFB | pdb_00009efb

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, HANGING DROP		289.15	300mM MgCl2, 100mM Tris pH 8.5, and 20%PEG-8k

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.019	α = 90
b = 48.962	β = 98.631
c = 85.302	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		2024-07-25	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	2.08	42.33	94.3	0.169	4.4	5.5		39356

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	2.08	5.64			0.319

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	2.4	42.216	25832	1367	94.786	0.187	0.1822	0.1881	0.2759	0.2747	36.87

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]
-2.252		-0.945	2.936		-0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.007
r_dihedral_angle_6_deg	14.522
r_lrange_other	8.861
r_lrange_it	8.844
r_dihedral_angle_2_deg	8.527
r_dihedral_angle_1_deg	6.988
r_scangle_it	5.813
r_scangle_other	5.812
r_mcangle_other	4.792
r_mcangle_it	4.791
r_scbond_it	3.597
r_scbond_other	3.597
r_mcbond_it	3.022
r_mcbond_other	3.02
r_angle_refined_deg	1.543
r_angle_other_deg	0.52
r_symmetry_xyhbond_nbd_refined	0.283
r_nbd_refined	0.222
r_symmetry_nbd_refined	0.211
r_symmetry_nbd_other	0.205
r_xyhbond_nbd_refined	0.191
r_nbtor_refined	0.18
r_nbd_other	0.174
r_symmetry_nbtor_other	0.081
r_metal_ion_refined	0.075
r_chiral_restr	0.07
r_symmetry_xyhbond_nbd_other	0.058
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5426
Nucleic Acid Atoms
Solvent Atoms	281
Heterogen Atoms	26

Software

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