3GZ9 | pdb_00003gz9

Crystal Structure of Peroxisome Proliferator-Activated Receptor Delta (PPARd) in Complex with a Full Agonist

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	289	15% PEG 8000, 0.2 M KCl, 1 mM EDTA, 25% propanediol, 0.5% heptanetriol, 1 mM DTT, 0.1 M Hepes, pH 7.5, vapor diffusion, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.81	56.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.577	α = 90
b = 92.129	β = 90
c = 39.555	γ = 90

Symmetry
Space Group	P 21 21 2

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	3X3 CCD ARRAY	2004-06-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.541	ALS	5.0.2

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	94.577	99.8	0.09	0.09	6.225	5.6	24154	24127		2	23.917

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2	2.11	99.5		0.37	0.37	2	5.3	3434

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2	94.49	2	24154	24127	1233	99.74	0.192	0.189	0.19	0.245	0.24	RANDOM	31.825

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]
-1.72			2.71		-1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.365
r_dihedral_angle_3_deg	17.791
r_dihedral_angle_4_deg	17.154
r_dihedral_angle_1_deg	6.474
r_scangle_it	5.418
r_scbond_it	3.639
r_mcangle_it	2.354
r_angle_refined_deg	2.202
r_mcbond_it	1.396
r_chiral_restr	0.139

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.365
r_dihedral_angle_3_deg	17.791
r_dihedral_angle_4_deg	17.154
r_dihedral_angle_1_deg	6.474
r_scangle_it	5.418
r_scbond_it	3.639
r_mcangle_it	2.354
r_angle_refined_deg	2.202
r_mcbond_it	1.396
r_chiral_restr	0.139
r_bond_refined_d	0.026
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2115
Nucleic Acid Atoms
Solvent Atoms	172
Heterogen Atoms	55

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

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.