8B93 | pdb_00008b93

Crystal structure of PPARG and NCOR2 with an inverse agonist (compound 15b)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		internal

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	PEG 3350 20%, HCOONa 0.2 M

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.979	α = 90
b = 85.479	β = 90
c = 121.588	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2021-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.0332	PETRA III, DESY	P11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	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	2.21	45.53	91.8	0.334	0.971	3.79	5.5		29412

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.21	2.34	90.8		1.374	0.625	1.6	5.3

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	internal	2.21	45.53	27941	1471	91.75	0.2788	0.2734	0.2764	0.3857	0.39	RANDOM	42.357

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]
0.09			0.49		-0.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.722
r_dihedral_angle_3_deg	19.468
r_dihedral_angle_4_deg	19.273
r_dihedral_angle_1_deg	6.595
r_angle_refined_deg	1.639
r_angle_other_deg	1.208
r_chiral_restr	0.071
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_gen_planes_other	0.007
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4072
Nucleic Acid Atoms
Solvent Atoms	63
Heterogen Atoms	76

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHASER	phasing