3KDT

Crystal structure of peroxisome proliferator-activatedeceptor alpha (PPARalpha) complex with N-3-((2-(4-Chlorophenyl)-5-methyl-1,3-oxazol-4-yl)methoxy)benzyl)-N-(methoxycarbonyl)glycine

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		298	PEG 4000, Ammonium and magnesium acetate, VAPOR DIFFUSION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.754	α = 90
b = 64.754	β = 90
c = 123.664	γ = 90

Symmetry
Space Group	P 41

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315		2004-04-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.1000	NSLS	X25

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.7	50	99	0.079	0.079	17.6	3.5		13931

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)
	2.7	2.8	99.7		0.429	2.8	3.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	2.7	50	13908	691	99.05	0.256	0.253	0.316	RANDOM	57.948

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]
2.49			2.49		-4.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.131
r_dihedral_angle_3_deg	17.856
r_dihedral_angle_4_deg	9.335
r_dihedral_angle_1_deg	5.89
r_scangle_it	1.541
r_angle_refined_deg	1.169
r_mcangle_it	0.99
r_scbond_it	0.944
r_mcbond_it	0.562
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.131
r_dihedral_angle_3_deg	17.856
r_dihedral_angle_4_deg	9.335
r_dihedral_angle_1_deg	5.89
r_scangle_it	1.541
r_angle_refined_deg	1.169
r_mcangle_it	0.99
r_scbond_it	0.944
r_mcbond_it	0.562
r_nbtor_refined	0.304
r_symmetry_vdw_refined	0.234
r_nbd_refined	0.218
r_xyhbond_nbd_refined	0.166
r_chiral_restr	0.082
r_symmetry_hbond_refined	0.059
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4181
Nucleic Acid Atoms
Solvent Atoms	2
Heterogen Atoms	62

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.