2Q5P | pdb_00002q5p

Crystal Structure of PPARgamma bound to partial agonist MRL24

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1KNU	PDB entry 1KNU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	1.4M sodium citrate, 0.125M Tris 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.355	α = 90
b = 61.452	β = 102.42
c = 117.947	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	CCD	MARMOSAIC 300 mm CCD	mirrors		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.9764	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.3	15	91.7	0.049	0.049	25.4	6.3	26218	26218			49.23

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.3	2.38	63.5		0.119	0.119	10.4	4.4	1780

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	PDB entry 1KNU	2.3	10	25937	25937	1273	91.88	0.208	0.206	0.2673	0.247	0.3079	RANDOM	44.242

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]
-0.01		0.11	0.39		-0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.923
r_dihedral_angle_4_deg	20.108
r_dihedral_angle_3_deg	17.144
r_dihedral_angle_1_deg	5.53
r_scangle_it	2.235
r_scbond_it	1.437
r_angle_refined_deg	1.303
r_mcangle_it	0.918
r_mcbond_it	0.576
r_nbtor_refined	0.305
r_symmetry_vdw_refined	0.223
r_nbd_refined	0.216
r_symmetry_hbond_refined	0.158
r_xyhbond_nbd_refined	0.154
r_chiral_restr	0.087
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4047
Nucleic Acid Atoms
Solvent Atoms	100
Heterogen Atoms	76

Software

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