6L89 | pdb_00006l89

Human PPARgamma ligand binding domain complexed with Butyrolactone 1

X-RAY DIFFRACTION

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Starting Model(s)

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

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
2.55	51.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.623	α = 90
b = 61.124	β = 103.643
c = 119.762	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 EIGER2 X 9M		2019-06-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 5C (4A)	1.00003	PAL/PLS	5C (4A)

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	50	99.3	0.032	39.3	4.6		38329

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	99.3		0.71		4.4

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	FREE R-VALUE	3WMH	2.1	48.975	34390	1734	88.996	0.231	0.2286	0.23	0.2693	0.28	33.139

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]
-0.132		-0.108	0.412		-0.204

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.942
r_dihedral_angle_4_deg	17.215
r_dihedral_angle_3_deg	13.548
r_lrange_it	5.871
r_lrange_other	5.862
r_dihedral_angle_1_deg	5.437
r_mcangle_it	3.013
r_mcangle_other	3.013
r_scangle_it	3.004
r_scangle_other	3.003
r_scbond_it	1.74
r_scbond_other	1.74
r_mcbond_it	1.737
r_mcbond_other	1.737
r_angle_refined_deg	1.237
r_angle_other_deg	1.203
r_nbd_other	0.23
r_symmetry_nbd_refined	0.222
r_nbd_refined	0.199
r_symmetry_nbd_other	0.188
r_xyhbond_nbd_refined	0.169
r_nbtor_refined	0.153
r_symmetry_xyhbond_nbd_refined	0.117
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.051
r_chiral_restr_other	0.036
r_symmetry_xyhbond_nbd_other	0.036
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4115
Nucleic Acid Atoms
Solvent Atoms	148
Heterogen Atoms	62

Software

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