7G04 | pdb_00007g04

Crystal Structure of human FABP5 in complex with 7-(4-chlorophenyl)-1,2,3,4-tetrahydronaphthalene-1-carboxylic acid, i.e. SMILES c12c(ccc(c2)c2ccc(cc2)Cl)CCC[C@H]1C(=O)O with IC50=3.3 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
2.32	47.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.391	α = 90
b = 62.906	β = 90
c = 74.407	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		2011-05-07	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	1.39	48.04	99.6	0.073	0.073	0.074	0.998	10.33	6.14		58462			26.792

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	1.4	1.44	100		1.502	1.626	0.465	1.25	6.82

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	1.4	48.04	52777	2826	96.88	0.1914	0.1899	0.1931	0.2197	0.2214	RANDOM	20.773

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]
0.03			-0.54		0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.878
r_dihedral_angle_4_deg	21.326
r_dihedral_angle_3_deg	13.024
r_dihedral_angle_1_deg	6.299
r_angle_refined_deg	1.957
r_angle_other_deg	1.123
r_chiral_restr	0.116
r_bond_refined_d	0.019
r_gen_planes_refined	0.009
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.878
r_dihedral_angle_4_deg	21.326
r_dihedral_angle_3_deg	13.024
r_dihedral_angle_1_deg	6.299
r_angle_refined_deg	1.957
r_angle_other_deg	1.123
r_chiral_restr	0.116
r_bond_refined_d	0.019
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2094
Nucleic Acid Atoms
Solvent Atoms	230
Heterogen Atoms	30

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.