7FYS | pdb_00007fys

Crystal Structure of human FABP4 in complex with 7-(4-methoxyphenyl)-1,8-dithia-3-azaspiro[4.5]dec-6-ene-2,4-dione, i.e. SMILES [C@@]12(C=C(c3ccc(cc3)OC)SCC2)SC(=O)NC1=O with IC50=4.5 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
2.19	43.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.51	α = 90
b = 53.896	β = 90
c = 74.953	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		2011-12-11	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	43.76	99.9	0.038	0.038	0.041	1	16.96	6.57		62311			14.884

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	99.9		1.105	1.197	0.698	1.69	6.788

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	43.77	57277	3142	97.03	0.1487	0.1471	0.1444	0.1779	0.1747	RANDOM	16.434

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]
0.1			-0.08		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.757
r_sphericity_free	22.159
r_dihedral_angle_4_deg	16.316
r_dihedral_angle_3_deg	14.975
r_sphericity_bonded	12.385
r_dihedral_angle_1_deg	6.235
r_rigid_bond_restr	5.777
r_angle_refined_deg	2.326
r_angle_other_deg	0.891
r_chiral_restr	0.137

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.757
r_sphericity_free	22.159
r_dihedral_angle_4_deg	16.316
r_dihedral_angle_3_deg	14.975
r_sphericity_bonded	12.385
r_dihedral_angle_1_deg	6.235
r_rigid_bond_restr	5.777
r_angle_refined_deg	2.326
r_angle_other_deg	0.891
r_chiral_restr	0.137
r_bond_refined_d	0.024
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	1046
Nucleic Acid Atoms
Solvent Atoms	200
Heterogen Atoms	42

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.