2Q5S | pdb_00002q5s

Crystal Structure of PPARgamma bound to partial agonist nTZDpa

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 Tris8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.712	α = 90
b = 62.194	β = 101.05
c = 117.956	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 325 mm CCD	mirror		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.9537	SSRL	BL11-1

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	2.05	20	99.3	0.055	0.055	33.4	6.9	39912	39912			30.79

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)
1	2.05	2.12	95.3		0.344	0.344	3.4	4.4	3805

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	2.05	9.97	39571	39571	1992	99.29	0.199	0.197	0.1958	0.245	0.2397	RANDOM	24.836

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]
-0.03			-0.04		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.616
r_dihedral_angle_4_deg	20.696
r_dihedral_angle_3_deg	16.439
r_dihedral_angle_1_deg	10.701
r_scangle_it	2.415
r_scbond_it	1.767
r_angle_refined_deg	1.354
r_mcangle_it	1.02
r_mcbond_it	0.857
r_symmetry_hbond_refined	0.458
r_nbtor_refined	0.305
r_symmetry_vdw_refined	0.256
r_nbd_refined	0.213
r_xyhbond_nbd_refined	0.169
r_chiral_restr	0.147
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4052
Nucleic Acid Atoms
Solvent Atoms	264
Heterogen Atoms	56

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