2ZY0

Crystal structure of the human RXR alpha ligand binding domain bound to a synthetic agonist compound and a coactivator peptide

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	290	10mM Tris-HCl, 250mM NaCl, 5mM DTT, 50mM calcium acetate, 18% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.975	α = 90
b = 66.85	β = 90
c = 110.793	γ = 90

Symmetry
Space Group	P 21 21 21

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		2007-09-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.933	ESRF	ID14-2

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	2.9	50	99.7	0.081	36.767	7	11166	11166			65.993

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)
	2.9	3	100		0.317		7.2	1094

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-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	PDB ENTRY 1MZN	2.9	10	10834	512	99.58	0.221	0.221	0.217	0.289	RANDOM	48.367

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]
5.37			-1.6		-3.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.676
r_dihedral_angle_4_deg	23.301
r_dihedral_angle_3_deg	15.385
r_dihedral_angle_1_deg	4.309
r_angle_refined_deg	1.043
r_scangle_it	0.88
r_scbond_it	0.552
r_mcangle_it	0.502
r_nbtor_refined	0.293
r_mcbond_it	0.268

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.676
r_dihedral_angle_4_deg	23.301
r_dihedral_angle_3_deg	15.385
r_dihedral_angle_1_deg	4.309
r_angle_refined_deg	1.043
r_scangle_it	0.88
r_scbond_it	0.552
r_mcangle_it	0.502
r_nbtor_refined	0.293
r_mcbond_it	0.268
r_nbd_refined	0.178
r_symmetry_vdw_refined	0.166
r_xyhbond_nbd_refined	0.128
r_chiral_restr	0.069
r_symmetry_hbond_refined	0.049
r_bond_refined_d	0.006
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3601
Nucleic Acid Atoms
Solvent Atoms	26
Heterogen Atoms	54

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.