7G09 | pdb_00007g09

Crystal Structure of human FABP4 in complex with 8-(3-bromophenyl)-7,9-dioxa-1-thia-3-azaspiro[4.5]decane-2,4-dione, i.e. SMILES [C@@]12(C(=O)NC(=O)S1)CO[C@@H](OC2)c1cc(ccc1)Br with IC50=2.3 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
2.21	44.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.494	α = 90
b = 53.941	β = 90
c = 75.611	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	PSI PILATUS 6M		2012-02-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.700030	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	1.05	30.96	95.4	0.081	0.081	0.089	0.999	9.59	6.15		59985			13.842

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	1.05	1.08	95.1		1.785	1.926	0.59	1.36	6.996

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	1.05	30.96	54268	2890	90.98	0.1615	0.1598	0.1589	0.1943	0.1942	RANDOM	14.38

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]
0.24			-0.2		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.068
r_sphericity_free	24.26
r_dihedral_angle_4_deg	18.492
r_dihedral_angle_3_deg	14.502
r_sphericity_bonded	10.3
r_dihedral_angle_1_deg	6.079
r_rigid_bond_restr	3.439
r_angle_other_deg	3.364
r_angle_refined_deg	1.919
r_chiral_restr	0.098

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.068
r_sphericity_free	24.26
r_dihedral_angle_4_deg	18.492
r_dihedral_angle_3_deg	14.502
r_sphericity_bonded	10.3
r_dihedral_angle_1_deg	6.079
r_rigid_bond_restr	3.439
r_angle_other_deg	3.364
r_angle_refined_deg	1.919
r_chiral_restr	0.098
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1040
Nucleic Acid Atoms
Solvent Atoms	212
Heterogen Atoms	45

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.