7CXL | pdb_00007cxl

The ligand-free structure of human PPARgamma LBD S289C mutant in the presence of the SRC-1 coactivator peptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5GTP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	295	2.2 M sodium malonate (pH 7.0)

Crystal Properties
Matthews coefficient	Solvent content
2.86	56.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.867	α = 90
b = 53.163	β = 90
c = 53.682	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	CCD	ADSC QUANTUM 270		2018-07-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 7A (6B, 6C1)	0.97934	PAL/PLS	7A (6B, 6C1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.7	50	100	0.08	0.994	25.16	7.8		10850

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.75	100		0.608	0.88	4	8.2

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	5GTP	2.7	30.002	10740	580	99.187	0.239	0.2381	0.24	0.255	0.26	42.634

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]
0.128			0.079		-0.207

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.069
r_dihedral_angle_4_deg	15.424
r_dihedral_angle_3_deg	13.64
r_lrange_it	10.519
r_lrange_other	10.516
r_dihedral_angle_1_deg	5.401
r_scangle_it	4.809
r_scangle_other	4.808
r_mcangle_it	4.763
r_mcangle_other	4.761
r_mcbond_it	2.778
r_mcbond_other	2.778
r_scbond_it	2.748
r_scbond_other	2.747
r_angle_refined_deg	1.305
r_angle_other_deg	1.13
r_nbd_other	0.256
r_nbd_refined	0.212
r_xyhbond_nbd_refined	0.195
r_symmetry_nbd_other	0.183
r_symmetry_nbd_refined	0.174
r_nbtor_refined	0.157
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.052
r_symmetry_xyhbond_nbd_refined	0.044
r_bond_refined_d	0.01
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	2205
Nucleic Acid Atoms
Solvent Atoms	36
Heterogen Atoms	7

Software

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