8WFE | pdb_00008wfe

The Crystal Structure of PPARg from Biortus.

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1M MIB pH9.0, 25% PEG 1500

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.808	α = 90
b = 62.297	β = 101.73
c = 118.415	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 EIGER X 9M		2023-05-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.95374	CLSI	08ID-1

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	2.2	49.03	97.9	0.051	16.6	7		32713

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	2.2	2.27			0.751

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	2.2	49.03	32709	1613	97.665	0.219	0.2172	0.2191	0.2479	0.2553	68.427

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]
2.099		1.062	4.456		-6.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	12.404
r_dihedral_angle_3_deg	11.038
r_lrange_it	7.746
r_lrange_other	7.734
r_scangle_it	5.619
r_scangle_other	5.618
r_dihedral_angle_1_deg	5.142
r_mcangle_it	4.664
r_mcangle_other	4.664
r_dihedral_angle_2_deg	4.066
r_scbond_it	3.295
r_scbond_other	3.294
r_mcbond_it	2.972
r_mcbond_other	2.97
r_angle_refined_deg	0.916
r_angle_other_deg	0.342
r_nbd_refined	0.209
r_symmetry_nbd_refined	0.189
r_symmetry_xyhbond_nbd_refined	0.185
r_nbtor_refined	0.175
r_symmetry_nbd_other	0.168
r_nbd_other	0.144
r_xyhbond_nbd_refined	0.133
r_symmetry_nbtor_other	0.069
r_chiral_restr	0.047
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4131
Nucleic Acid Atoms
Solvent Atoms	101
Heterogen Atoms	18

Software

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