7EFQ

Crystal structure of hPPARgamma ligand binding domain complexed with rosiglitazone-based fluorescence probe

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	One microliter of PPARgamma-LBD solution (6 mg/mL, in 20 mM Tris-HCl pH 8.0, 1 mM TCEP, 0.5 mM EDTA) with 0.5 equiv. ligand with 1 microliter of reservoir solution (0.8 M sodium citrate and 0.1 M Tris-HCl pH 7.3). Drops were equilibrated against 300 microliter of reservoir solution at 293K.

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.33	α = 90
b = 61.9	β = 102.29
c = 119.37	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	PIXEL	DECTRIS PILATUS3 S 2M		2020-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.000	Photon Factory	BL-5A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.3	26.75	99.1	0.043	0.06	0.042	0.998	14.1	3		29512

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.38			0.348	0.481	0.331	0.858		2.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2vv3	2.3	26.75	29502	1515	98.904	0.226	0.2243	0.2644	49.828

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]
-0.595		0.453	0.218		0.165

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.232
r_dihedral_angle_4_deg	20.541
r_dihedral_angle_3_deg	19.355
r_dihedral_angle_1_deg	6.761
r_lrange_it	4.794
r_lrange_other	4.792
r_scangle_it	3.427
r_scangle_other	3.427
r_mcangle_other	2.658
r_mcangle_it	2.657
r_scbond_it	2.211
r_scbond_other	2.21
r_angle_refined_deg	1.886
r_mcbond_it	1.774
r_mcbond_other	1.748
r_angle_other_deg	1.378
r_nbd_refined	0.235
r_symmetry_nbd_refined	0.229
r_nbd_other	0.223
r_symmetry_nbd_other	0.199
r_nbtor_refined	0.175
r_symmetry_xyhbond_nbd_refined	0.122
r_xyhbond_nbd_refined	0.121
r_chiral_restr	0.088
r_symmetry_nbtor_other	0.088
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_gen_planes_other	0.005
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4058
Nucleic Acid Atoms
Solvent Atoms	72
Heterogen Atoms	35

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
pointless	data reduction
PHASER	phasing
Coot	model building