9OLC | pdb_00009olc

Crystal structure of PPARg ligand-binding domain in complex with NCoR1 peptide and FTX-6746

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6ONI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	0.1 M MES pH 6.5, 0.1M Ammonium Sulfate, 24% PEG8000

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.13	α = 101.193
b = 70.33	β = 106.579
c = 92.68	γ = 104.98

Symmetry
Space Group	P 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	PIXEL	DECTRIS EIGER X 9M		2021-03-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.12713	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.83	48.046	90	0.995	5.1	3.7		25524

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.83	2.98			0.889

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.83	48.046	24151	1159	85.183	0.234	0.2309	0.2349	0.2983	0.299	86.128

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]
-3.222	2.106	-1.876	9.688	0.423	-5.469

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.438
r_lrange_it	14.68
r_lrange_other	14.679
r_dihedral_angle_6_deg	14.56
r_scangle_it	10.895
r_scangle_other	10.894
r_mcangle_it	10.59
r_mcangle_other	10.59
r_mcbond_it	6.891
r_mcbond_other	6.89
r_scbond_it	6.808
r_scbond_other	6.808
r_dihedral_angle_1_deg	5.695
r_dihedral_angle_other_3_deg	5.286
r_dihedral_angle_2_deg	4.8
r_angle_refined_deg	1.355
r_angle_other_deg	0.462
r_nbd_refined	0.229
r_nbd_other	0.213
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.185
r_symmetry_nbd_refined	0.173
r_xyhbond_nbd_refined	0.167
r_symmetry_xyhbond_nbd_refined	0.144
r_ncsr_local_group_3	0.104
r_ncsr_local_group_5	0.102
r_ncsr_local_group_6	0.102
r_ncsr_local_group_8	0.1
r_ncsr_local_group_9	0.095
r_ncsr_local_group_2	0.092
r_ncsr_local_group_7	0.092
r_ncsr_local_group_4	0.086
r_ncsr_local_group_1	0.078
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.061
r_chiral_restr_other	0.032
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7842
Nucleic Acid Atoms
Solvent Atoms	8
Heterogen Atoms	63

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing