3ET2 | pdb_00003et2

Structure of PPARdelta with 3-[5-Methoxy-1-(4-methoxy-benzenesulfonyl)-1H-indol-3-yl]-propionic acid

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GWX	PDB entry 1GWX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5	277	The purified PPARd LBD protein was diluted to 10mg/ml and 1mM of indeglitazar was added to the diluted protein prior to crystallization by mixing equal volumes of protein/compound sample with reservoir solution containing 16% PEG 3350, 0.1 M Tris buffer at pH 7.5, 0.2 M magnesium chloride, and 1% n-butanol, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.402	α = 90
b = 94.353	β = 98.27
c = 97.183	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	CCD	ADSC QUANTUM 210		2006-05-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1		ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	2.24	50	98.8	0.098		3.3		33526

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.24	2.3			0.489	1	3.3	4927

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB entry 1GWX	2.24	38.99	1.35	33911	33474	1689	98.7	0.188	0.185	0.1821	0.242	0.2407

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]
-0.7778		2.334	7.1072		-8.8198

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.82
f_angle_d	1.08
f_chiral_restr	0.06
f_bond_d
f_plane_restr

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4287
Nucleic Acid Atoms
Solvent Atoms	372
Heterogen Atoms	69

Software

Software
Software Name	Purpose
Blu-Ice	data collection
CCP4	model building
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
CCP4	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.