6L8B

The ligand-free structure of human PPARgamma LBD

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3VSO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	295	1.2 M Sodium citrate tribasic dihydrate, 0.1 M HEPES pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.15	α = 90
b = 62.256	β = 102.508
c = 119.504	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 PILATUS 6M		2019-03-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 11C	0.97941	PAL/PLS	11C

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	2.1	30	98	0.101	12.625	4.6		38322

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	2.1	2.14			0.583

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3VSO	2.102	29.345	35593	1769	90.889	0.221	0.2181	0.2675	29.241

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]
0.357		-0.048	0.133		-0.427

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.651
r_dihedral_angle_4_deg	17.137
r_dihedral_angle_3_deg	13.383
r_dihedral_angle_1_deg	5.288
r_lrange_it	4.953
r_lrange_other	4.945
r_scangle_it	2.445
r_scangle_other	2.444
r_mcangle_it	2.339
r_mcangle_other	2.338
r_angle_other_deg	2.221
r_scbond_it	1.443
r_scbond_other	1.443
r_mcbond_it	1.352
r_mcbond_other	1.352
r_angle_refined_deg	1.198
r_nbd_other	0.26
r_symmetry_nbd_refined	0.22
r_symmetry_nbd_other	0.205
r_symmetry_xyhbond_nbd_refined	0.203
r_nbd_refined	0.192
r_xyhbond_nbd_refined	0.168
r_nbtor_refined	0.15
r_symmetry_xyhbond_nbd_other	0.058
r_symmetry_nbtor_other	0.056
r_chiral_restr	0.05
r_bond_other_d	0.034
r_gen_planes_other	0.005
r_gen_planes_refined	0.004
r_bond_refined_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4208
Nucleic Acid Atoms
Solvent Atoms	159
Heterogen Atoms

Software

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