3U9Q

Ligand binding domain of PPARgamma complexed with Decanoic Acid and PGC-1a peptide

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.2	298	0.2 M sodium acetate (pH 6.2), 20% PEG 3350, 15% glycerol and 1 mM concentration of the ligand., VAPOR DIFFUSION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.726	α = 90
b = 54.346	β = 107.52
c = 66.809	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	200	CCD	MARMOSAIC 300 mm CCD		2009-06-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D		APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.52	33.082	94.9			45773	43465	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.522	1.562	97.64

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.522	30.082	2	45773	43465	2308	99.73	0.221	0.1851	0.1831	0.2221	RANDOM	20.037

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		-0.2	-0.27		-0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.244
r_dihedral_angle_4_deg	18.723
r_dihedral_angle_3_deg	13.173
r_scangle_it	5.265
r_dihedral_angle_1_deg	5.089
r_scbond_it	3.181
r_mcangle_it	2.03
r_angle_refined_deg	1.654
r_mcbond_it	1.078
r_chiral_restr	0.113

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.244
r_dihedral_angle_4_deg	18.723
r_dihedral_angle_3_deg	13.173
r_scangle_it	5.265
r_dihedral_angle_1_deg	5.089
r_scbond_it	3.181
r_mcangle_it	2.03
r_angle_refined_deg	1.654
r_mcbond_it	1.078
r_chiral_restr	0.113
r_bond_refined_d	0.015
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2123
Nucleic Acid Atoms
Solvent Atoms	394
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
HKL-2000	data scaling
PHASER	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.