6AD9

Crystal Structure of PPARgamma Ligand Binding Domain in complex with dibenzooxepine derivative compound-9

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	293	0.5M LiCl, 0.1M Tris-HCl pH 8.5, 28% PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.73	α = 90
b = 54.338	β = 108.61
c = 66.77	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	100	CCD	ADSC QUANTUM 315		2009-03-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.00000	Photon Factory	BL-5A

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	2.2	50	99.8	0.17	4.5	3.7		15196

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)
1	2.2	2.28	100		0.614		3.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.2	50	14420	762	99.7	0.1874	0.18451	0.2399	RANDOM	27.867

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]
-0.68		-0.6	0.33		0.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.225
r_dihedral_angle_4_deg	15.942
r_dihedral_angle_3_deg	15.928
r_long_range_B_refined	6.294
r_long_range_B_other	6.293
r_dihedral_angle_1_deg	5.898
r_scangle_other	4.412
r_mcangle_other	3.276
r_mcangle_it	3.273
r_scbond_it	2.745
r_scbond_other	2.744
r_mcbond_it	2.094
r_mcbond_other	2.083
r_angle_refined_deg	1.72
r_angle_other_deg	1.027
r_chiral_restr	0.107
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2117
Nucleic Acid Atoms
Solvent Atoms	187
Heterogen Atoms	37

Software

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