2P4Y | pdb_00002p4y

Crystal structure of human PPAR-gamma-ligand binding domain complexed with an indole-based modulator

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		SE-MET PPAR-GAMMA-LBD COMPLEX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	298	0.95M Trisodium citrate, 0.1M Tris-HCl pH 8.5, 1mM TCEP, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.148	α = 90
b = 59.859	β = 103.76
c = 118.287	γ = 90

Symmetry
Space Group	C 1 2 1

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 210		2002-04-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.00000	APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.25	40.34	99	0.09	15.6	5	29974	29681			29.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.25	2.35	93.7		0.3533	2.51		3407

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	SE-MET PPAR-GAMMA-LBD COMPLEX	2.25	40.34	28327	28327	1402	94.5	0.232	0.232	0.232	0.23	0.274	0.27	RANDOM	43.5

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]
-8.41		2.34	9.36		-0.95

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	20.6
c_scangle_it	3.37
c_mcangle_it	2.3
c_scbond_it	2.23
c_mcbond_it	1.45
c_angle_deg	0.9
c_improper_angle_d	0.66
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3792
Nucleic Acid Atoms
Solvent Atoms	93
Heterogen Atoms	88

Software

Software
Software Name	Purpose
CNX	refinement
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
CNX	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.