7G13 | pdb_00007g13

Crystal Structure of human FABP4 binding site mutated to that of FABP5 in complex with 4-[[3-(3-cyclopropyl-1,2,4-oxadiazol-5-yl)-4,5,6,7-tetrahydro-1-benzothiophen-2-yl]carbamoyl]-3,6-dihydro-2H-pyran-5-carboxylic acid, i.e. SMILES S1C(=C(C2=NC(=NO2)C2CC2)C2=C1CCCC2)NC(=O)C1=C(COCC1)C(=O)O with IC50=0.119472 microM

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		inhouse model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	protein in 25mM Tris/HCl pH 7.5 100mM NaCl, see also PMID 27658368

Crystal Properties
Matthews coefficient	Solvent content
2.05	39.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.141	α = 90
b = 53.024	β = 90
c = 72.169	γ = 90

Symmetry
Space Group	P 2 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	PSI PILATUS 6M		2012-06-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.000000	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim 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	1.15	42.73	98.9	0.093	0.093	0.117	0.998	10.49	6.03		44200			15.027

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.15	1.18	96		1.376	1.506	0.494	1.38	6.018

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	inhouse model	1.15	42.73	39948	2156	94.34	0.1599	0.1579	0.1553	0.1981	0.1971	RANDOM	13.857

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]
0.4			0.67		-1.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.908
r_sphericity_free	24.599
r_dihedral_angle_4_deg	16.304
r_dihedral_angle_3_deg	13.911
r_sphericity_bonded	12.86
r_dihedral_angle_1_deg	6.417
r_rigid_bond_restr	5.127
r_angle_other_deg	3.346
r_angle_refined_deg	2.283
r_chiral_restr	0.134

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.908
r_sphericity_free	24.599
r_dihedral_angle_4_deg	16.304
r_dihedral_angle_3_deg	13.911
r_sphericity_bonded	12.86
r_dihedral_angle_1_deg	6.417
r_rigid_bond_restr	5.127
r_angle_other_deg	3.346
r_angle_refined_deg	2.283
r_chiral_restr	0.134
r_bond_refined_d	0.02
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1012
Nucleic Acid Atoms
Solvent Atoms	208
Heterogen Atoms	62

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
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.