7G1K | pdb_00007g1k

Crystal Structure of human FABP4 in complex with 4-(4-fluorophenyl)sulfanyl-6-methyl-2-phenylpyrimidine-5-carboxylic acid, i.e. SMILES c1(c(c(nc(n1)c1ccccc1)C)C(=O)O)Sc1ccc(cc1)F with IC50=0.867 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
2.17	43.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.391	α = 90
b = 53.685	β = 90
c = 75.026	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		2011-10-22	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	1.12	37.51	99.1	0.032	0.032	0.031	1	22.04	6.04		50489			15.079

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	1.12	1.15	89.2		0.293	0.329	0.947	4.99	4.486

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	1.12	37.5	47284	2514	97.9	0.1364	0.135	0.138	0.1623	0.1606	RANDOM	13

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]
0.31			-0.42		0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.851
r_sphericity_free	19.406
r_dihedral_angle_4_deg	15.523
r_dihedral_angle_3_deg	12.983
r_sphericity_bonded	9.862
r_dihedral_angle_1_deg	6.605
r_rigid_bond_restr	5.684
r_angle_refined_deg	2.143
r_angle_other_deg	1.524
r_chiral_restr	0.135

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.851
r_sphericity_free	19.406
r_dihedral_angle_4_deg	15.523
r_dihedral_angle_3_deg	12.983
r_sphericity_bonded	9.862
r_dihedral_angle_1_deg	6.605
r_rigid_bond_restr	5.684
r_angle_refined_deg	2.143
r_angle_other_deg	1.524
r_chiral_restr	0.135
r_bond_refined_d	0.021
r_gen_planes_refined	0.014
r_bond_other_d	0.008
r_gen_planes_other	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1040
Nucleic Acid Atoms
Solvent Atoms	175
Heterogen Atoms	65

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.