9MAH | pdb_00009mah

PPARG-Spermine analogs

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4EMA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	1.0 M Na3citrate, 0.1 M Imidazole pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.997	α = 90
b = 62.46	β = 100.628
c = 118.055	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 16M		2024-10-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	0.999990	SPring-8	BL45XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	48.65	98.4	0.995	10.6	6.5		37104

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.16			0.806

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	2.1	48.65	37100	1899	98.133	0.187	0.1845	0.1917	0.2336	0.2374	45.236

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]
-1.297		1.642	0.735		-0.051

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.955
r_dihedral_angle_3_deg	13.304
r_dihedral_angle_2_deg	12.849
r_lrange_it	10.384
r_lrange_other	10.373
r_scangle_it	8.267
r_scangle_other	8.265
r_mcangle_it	5.832
r_mcangle_other	5.831
r_dihedral_angle_1_deg	5.516
r_scbond_it	5.25
r_scbond_other	5.249
r_mcbond_it	4.054
r_mcbond_other	4.054
r_angle_refined_deg	1.566
r_angle_other_deg	0.531
r_nbd_refined	0.235
r_nbd_other	0.189
r_symmetry_nbd_other	0.187
r_symmetry_nbd_refined	0.186
r_nbtor_refined	0.183
r_xyhbond_nbd_refined	0.176
r_ncsr_local_group_1	0.119
r_symmetry_xyhbond_nbd_other	0.102
r_chiral_restr	0.079
r_symmetry_nbtor_other	0.073
r_chiral_restr_other	0.022
r_symmetry_xyhbond_nbd_refined	0.021
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4115
Nucleic Acid Atoms
Solvent Atoms	182
Heterogen Atoms	41

Software

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