4Y29 | pdb_00004y29

Identification of a novel PPARg ligand that regulates metabolism

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3U9Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293.15	0.2 M Sodium thiocyanate, 20% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.624	α = 90
b = 54.514	β = 107.07
c = 66.402	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 315r		2013-05-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	1.0050	SSRF	BL17U

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	1.98	50	99.9	0.068	11.6	5.3		21090

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	1.98	2.01	100		0.356		5.2	1051

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	3U9Q	1.98	41.36	19842	1068	99.94	0.1791	0.177	0.1773	0.2187	0.2187	RANDOM	26.6

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]
-0.01		0.02	0.02		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.019
r_dihedral_angle_4_deg	15.788
r_dihedral_angle_3_deg	14.554
r_scangle_it	6.77
r_dihedral_angle_1_deg	5.853
r_scbond_it	4.056
r_mcangle_it	2.77
r_angle_refined_deg	2.069
r_mcbond_it	1.536
r_chiral_restr	0.148
r_bond_refined_d	0.026
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2135
Nucleic Acid Atoms
Solvent Atoms	197
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction