9L3T | pdb_00009l3t

PPARgamma Ligand binding domain in complex with piperine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VV3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	0.1 M Tris-HCl, 0.7 M sodium citrate

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.43	α = 90
b = 62.02	β = 102.09
c = 119.49	γ = 90

Symmetry
Space Group	C 1 2 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 PILATUS3 S 6M		2024-04-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0000	Photon Factory	BL-5A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	Rpim 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	2.36	45.68	99.6	0.058	0.04	0.995	9.2	3.1		27580

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.36	2.45			0.344	0.236	0.936	2.6	2.9

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	THROUGHOUT	2VV3	2.36	45.68	27570	1374	99.391	0.203	0.2006	0.1997	0.2547	0.2601	68.131

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]
2.682		0.29	-0.376		-2.226

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.094
r_dihedral_angle_6_deg	15.525
r_dihedral_angle_2_deg	11.649
r_lrange_it	10.089
r_lrange_other	10.089
r_scangle_it	8.318
r_scangle_other	8.317
r_dihedral_angle_1_deg	6.064
r_mcangle_it	5.985
r_mcangle_other	5.985
r_scbond_it	5.658
r_scbond_other	5.657
r_mcbond_it	4.336
r_mcbond_other	4.335
r_angle_refined_deg	2.2
r_angle_other_deg	0.721
r_nbd_refined	0.254
r_nbd_other	0.252
r_chiral_restr_other	0.238
r_symmetry_xyhbond_nbd_refined	0.214
r_symmetry_nbd_other	0.203
r_nbtor_refined	0.193
r_xyhbond_nbd_refined	0.174
r_ncsr_local_group_1	0.16
r_symmetry_nbd_refined	0.146
r_chiral_restr	0.104
r_symmetry_nbtor_other	0.083
r_symmetry_xyhbond_nbd_other	0.05
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4054
Nucleic Acid Atoms
Solvent Atoms	36
Heterogen Atoms	21

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
iMOSFLM	data reduction
REFMAC	phasing