5GTP | pdb_00005gtp

The agonist-free structure of human PPARgamma ligand binding domain in the presence of the SRC-1 coactivator peptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3VN2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	296	2.2 M sodium malonate (pH 7.0)

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.31	α = 90
b = 53.062	β = 90
c = 53.552	γ = 90

Symmetry
Space Group	P 21 21 2

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 270		2014-05-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 7A (6B, 6C1)	0.97934	PAL/PLS	7A (6B, 6C1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.35	50	99.4	36.2	5.8		16193

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	2.35	2.39	100		0.603	4	6.1

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	3VN2	2.35	30	15328	817	99.43	0.21292	0.21066	0.22	0.25809	0.26	RANDOM	67.958

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]
-2.54			0.82		1.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.648
r_dihedral_angle_4_deg	22.439
r_dihedral_angle_3_deg	14.4
r_long_range_B_refined	11.45
r_long_range_B_other	11.449
r_scangle_other	8.449
r_mcangle_it	7.147
r_mcangle_other	7.145
r_dihedral_angle_1_deg	5.614
r_scbond_it	5.282
r_scbond_other	5.281
r_mcbond_it	4.82
r_mcbond_other	4.817
r_angle_refined_deg	1.496
r_angle_other_deg	1.181
r_chiral_restr	0.082
r_bond_refined_d	0.012
r_bond_other_d	0.006
r_gen_planes_refined	0.006
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	2196
Nucleic Acid Atoms
Solvent Atoms	45
Heterogen Atoms	22

Software

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