7MHD | pdb_00007mhd

Thioesterase Domain of Human Fatty Acid Synthase (FASN-TE) binding a competitive inhibitor SBP-7635

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3TJM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.3 ul of 8 mg/ml FASN-TE in 100 mM NaCl, 50 mM BisTris pH 6.0, 10 mM DTT, 0.5 mM of the inhibitor and 1% DMSO were mixed with 0.2 ul of well solution 10% PEG400, 50 mM TRIS-Cl pH 8.5, 1 mM DTT, 1 mM Ethylenediaminetetraacetic acid disodium salt (EDTA), 300 mM NaCl.

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.886	α = 90
b = 61.486	β = 90
c = 77.45	γ = 90

Symmetry
Space Group	P 21 21 21

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 PILATUS 6M		2016-05-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	1.0332	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	35.93	98.2	0.049	15.1	4.5		16885			39.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.03	2.08	82.5		0.618	2.1	3.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3TJM	2.03	35.93	16028	824	97.86	0.1956	0.1928	0.2	0.2457	0.25	RANDOM	42.494

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]
0.61			-1.91		1.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.782
r_dihedral_angle_4_deg	20.184
r_dihedral_angle_3_deg	15.43
r_dihedral_angle_1_deg	6.308
r_angle_refined_deg	1.526
r_angle_other_deg	1.289
r_chiral_restr	0.072
r_gen_planes_refined	0.008
r_bond_refined_d	0.007
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.782
r_dihedral_angle_4_deg	20.184
r_dihedral_angle_3_deg	15.43
r_dihedral_angle_1_deg	6.308
r_angle_refined_deg	1.526
r_angle_other_deg	1.289
r_chiral_restr	0.072
r_gen_planes_refined	0.008
r_bond_refined_d	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2189
Nucleic Acid Atoms
Solvent Atoms	106
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

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.