2VV3 | pdb_00002vv3

hPPARgamma Ligand binding domain in complex with 4-oxoDHA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2I4P	PDB ENTRY 2I4P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8	295	TRIS 100MM PH 8, 0.7M NA-CITRATE, 1MM TCEP, 0.5MM EDTA, VAPOUR DIFFUSION, DARK, UNDER NITROGEN, 22 DEGREES CELSIUS

Crystal Properties
Matthews coefficient	Solvent content
2.8	55.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.04	α = 90
b = 61.75	β = 103.18
c = 119.48	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 CCD		2007-11-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3		ESRF	ID14-3

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	2.85	58.12	98.5	0.14	8.4	2.8		28148		2	44.2

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	2.85	3	99.9		0.34	3.3	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 (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 2I4P	2.85	33.61	28148	1412	92	0.225	0.225	0.22	0.252	0.25	RANDOM	46.3

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]
1.09		2.66	12.6		-13.7

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	19.7
c_scangle_it	2.57
c_mcangle_it	2.08
c_scbond_it	1.63
c_angle_deg	1.2
c_mcbond_it	1.19
c_improper_angle_d	0.82
c_bond_d	0.01
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4025
Nucleic Acid Atoms
Solvent Atoms	80
Heterogen Atoms	25

Software

Software
Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing