2P1T

Crystal structure of the ligand binding domain of the retinoid X receptor alpha in complex with 3-(2'-methoxy)-tetrahydronaphtyl cinnamic acid and a fragment of the coactivator TIF-2

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	16% PEG 3350, 0.1M Tris, 1M ammonium acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.15	α = 90
b = 64.15	β = 90
c = 112.692	γ = 90

Symmetry
Space Group	P 43 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 4	Toroidal mirror	2007-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.8	37.5	99.9	0.066	8.3	12.1	22586	22530			18.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.8	1.9	99.9		0.28	2.5	10.8	3222

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1mvc	1.8	37	22586	21434	1152	99.92	0.198	0.198	0.197	0.218	RANDOM	15.413

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]
0.24			0.24		-0.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.37
r_dihedral_angle_4_deg	22.469
r_dihedral_angle_3_deg	12.881
r_dihedral_angle_1_deg	4.67
r_scangle_it	2.636
r_scbond_it	1.699
r_angle_refined_deg	1.147
r_mcangle_it	1.038
r_mcbond_it	0.599
r_symmetry_hbond_refined	0.336

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.37
r_dihedral_angle_4_deg	22.469
r_dihedral_angle_3_deg	12.881
r_dihedral_angle_1_deg	4.67
r_scangle_it	2.636
r_scbond_it	1.699
r_angle_refined_deg	1.147
r_mcangle_it	1.038
r_mcbond_it	0.599
r_symmetry_hbond_refined	0.336
r_nbtor_refined	0.303
r_nbd_refined	0.193
r_symmetry_vdw_refined	0.182
r_xyhbond_nbd_refined	0.096
r_chiral_restr	0.091
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1751
Nucleic Acid Atoms
Solvent Atoms	112
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.