7CXI

The ligand-free structure of human PPARgamma LBD F287Y mutant in the presence of the SRC-1 coactivator peptide

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5GTP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	295	2.2 M sodium malonate (pH 7.0)

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.748	α = 90
b = 52.377	β = 90
c = 53.973	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		2017-11-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 5C (4A)	0.97934	PAL/PLS	5C (4A)

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	2.3	50	99.6	0.054	31.8	7.7		17093

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	2.3	2.34	100		0.66	3.06	7.8

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5GTP	2.3	48.668	16498	831	96.221	0.245	0.2434	0.2761	41.091

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]
0.283			-0.158		-0.124

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.924
r_dihedral_angle_4_deg	18.822
r_dihedral_angle_3_deg	14.78
r_lrange_other	10.042
r_lrange_it	10.038
r_scangle_other	6.577
r_scangle_it	6.576
r_dihedral_angle_1_deg	6.201
r_mcangle_it	5.873
r_mcangle_other	5.871
r_scbond_other	3.73
r_scbond_it	3.728
r_mcbond_other	3.607
r_mcbond_it	3.606
r_angle_refined_deg	1.306
r_angle_other_deg	1.208
r_symmetry_nbd_refined	0.345
r_nbd_other	0.329
r_symmetry_xyhbond_nbd_refined	0.25
r_nbd_refined	0.215
r_symmetry_nbd_other	0.184
r_xyhbond_nbd_refined	0.174
r_nbtor_refined	0.156
r_symmetry_xyhbond_nbd_other	0.126
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.06
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2197
Nucleic Acid Atoms
Solvent Atoms	26
Heterogen Atoms	7

Software

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