7FY4 | pdb_00007fy4

Crystal Structure of human FABP4 binding site mutated to that of FABP5 in complex with 2-benzyl-6-tert-butyl-3-methyl-4-phenyl-5-(1H-tetrazol-5-yl)pyridine, i.e. SMILES N1C(=NN=N1)c1c(nc(c(c1c1ccccc1)C)Cc1ccccc1)C(C)(C)C with IC50=0.0608835 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
2.03	39.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.677	α = 90
b = 53.128	β = 90
c = 72.264	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		2012-08-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.700000	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	1.51	36.13	97.7	0.124	0.124	0.135	0.998	7.84	5.71		19384			27.849

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	1.51	1.55	100		1.856	2.013	0.42	1.15	6.698

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	1.51	36.13	17527	963	93.36	0.207	0.2027	0.2002	0.2862	0.287	RANDOM	22.226

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]
-0.94			0.25		0.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.478
r_sphericity_free	27.716
r_dihedral_angle_4_deg	17.831
r_sphericity_bonded	16.78
r_dihedral_angle_3_deg	15.852
r_dihedral_angle_1_deg	6.822
r_rigid_bond_restr	3.959
r_angle_refined_deg	1.651
r_chiral_restr	0.101
r_bond_refined_d	0.013

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.478
r_sphericity_free	27.716
r_dihedral_angle_4_deg	17.831
r_sphericity_bonded	16.78
r_dihedral_angle_3_deg	15.852
r_dihedral_angle_1_deg	6.822
r_rigid_bond_restr	3.959
r_angle_refined_deg	1.651
r_chiral_restr	0.101
r_bond_refined_d	0.013
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1012
Nucleic Acid Atoms
Solvent Atoms	85
Heterogen Atoms	29

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.