6KTN

Human PPARgamma ligand-binding domain R288A mutant in complex with imatinib

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	296	2.2 M sodium malonate (pH 7.0)

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.928	α = 90
b = 52.779	β = 90
c = 53.438	γ = 90

Symmetry
Space Group	P 21 21 2

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 2M-F		2018-05-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NE3A	1.0	Photon Factory	AR-NE3A

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	2.75	50	99.9	0.059	30.1	6.8		10176

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	2.75	2.8	99.6		0.679

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	6JQ7	2.752	30.002	9680	459	95.482	0.222	0.2205	0.2563	44.711

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]
0.559			-0.126		-0.433

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.657
r_dihedral_angle_4_deg	19.772
r_dihedral_angle_3_deg	16.702
r_lrange_it	9.128
r_lrange_other	9.126
r_dihedral_angle_1_deg	5.935
r_scangle_it	5.87
r_scangle_other	5.869
r_mcangle_it	5.367
r_mcangle_other	5.366
r_scbond_it	3.553
r_scbond_other	3.552
r_mcbond_it	3.209
r_mcbond_other	3.208
r_chiral_restr_other	1.719
r_angle_refined_deg	1.389
r_angle_other_deg	1.344
r_symmetry_xyhbond_nbd_refined	0.339
r_symmetry_nbd_refined	0.21
r_nbd_refined	0.209
r_nbd_other	0.203
r_symmetry_nbd_other	0.202
r_nbtor_refined	0.164
r_xyhbond_nbd_refined	0.157
r_symmetry_nbtor_other	0.096
r_chiral_restr	0.054
r_symmetry_xyhbond_nbd_other	0.024
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2216
Nucleic Acid Atoms
Solvent Atoms	30
Heterogen Atoms	37

Software

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