3VSP | pdb_00003vsp

Human PPAR gamma ligand binding domain in complex with a gamma selective agonist mekt28

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3AN3	pdb entry 3an3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	0.8M SODIUM CITRATE, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.409	α = 90
b = 60.871	β = 102.95
c = 118.598	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	ADSC QUANTUM 315		2011-01-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.0000	SPring-8	BL38B1

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	2.02	50	97.9	0.045		3.6		41981			37.5

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 (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 3an3	2.4	32.68	24974	1251	97.4	0.222	0.222	0.222	0.274	0.2742	RANDOM	52.2

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]
-8.7		3.75	21.62		-12.91

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	18.7
c_scangle_it	3.06
c_mcangle_it	2.27
c_scbond_it	2.12
c_mcbond_it	1.38
c_angle_deg	1.1
c_improper_angle_d	0.78
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4191
Nucleic Acid Atoms
Solvent Atoms	35
Heterogen Atoms	38

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing