2Q6R | pdb_00002q6r

Crystal structure of PPAR gamma complexed with partial agonist SF147

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1KNU	PDB Entry 1KNU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	1.4M sodium citrate, 0.125M Tris 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.8	α = 90
b = 62.255	β = 101.12
c = 118.071	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	MARMOSAIC 300 mm CCD	mirrors		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.9764	APS	22-ID

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	2.4	15	91.3	0.068	0.068	24.6	6.3	22911	22911			57.39

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)
	2.4	2.49	56.8		0.196	0.196	4.8	3.3	1413

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 (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	PDB Entry 1KNU	2.407	10	22642	22642	1146	90.91	0.27	0.269	0.2641	0.284	0.2748	RANDOM	88.97

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]
0.69		0.07	6.03		-6.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.929
r_dihedral_angle_3_deg	18.73
r_dihedral_angle_4_deg	16.954
r_dihedral_angle_1_deg	12.592
r_scangle_it	10.973
r_mcangle_it	9.548
r_scbond_it	6.915
r_mcbond_it	5.593
r_angle_refined_deg	1.616
r_xyhbond_nbd_refined	0.322
r_nbtor_refined	0.306
r_nbd_refined	0.234
r_chiral_restr	0.228
r_symmetry_vdw_refined	0.189
r_symmetry_hbond_refined	0.142
r_bond_refined_d	0.009
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3887
Nucleic Acid Atoms
Solvent Atoms	124
Heterogen Atoms	58

Software

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