7CXJ | pdb_00007cxj

The ligand-free structure of human PPARgamma LBD R288C mutant 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	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
2.74	59.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.248	α = 90
b = 52.878	β = 90
c = 53.887	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		2017-12-26	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)	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	2.65	50	99.6	0.069	28.03	7.7		11616

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.65	2.7			0.759	0.873

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5GTP	2.65	49.095	11194	571	97.781	0.241	0.2392	0.24	0.2753	0.28	39.247

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]
0.253			0.053		-0.307

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.904
r_dihedral_angle_4_deg	16.518
r_dihedral_angle_3_deg	13.714
r_lrange_it	7.662
r_lrange_other	7.66
r_dihedral_angle_1_deg	6.269
r_scangle_other	5.183
r_scangle_it	5.18
r_mcangle_it	4.473
r_mcangle_other	4.473
r_scbond_it	3.448
r_scbond_other	3.434
r_mcbond_it	2.627
r_mcbond_other	2.623
r_angle_other_deg	1.447
r_angle_refined_deg	1.244
r_symmetry_xyhbond_nbd_refined	0.313
r_nbd_other	0.308
r_symmetry_nbd_other	0.219
r_nbd_refined	0.215
r_xyhbond_nbd_refined	0.173
r_nbtor_refined	0.169
r_symmetry_nbd_refined	0.111
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.063
r_bond_refined_d	0.006
r_symmetry_xyhbond_nbd_other	0.005
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2168
Nucleic Acid Atoms
Solvent Atoms	19
Heterogen Atoms

Software

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