3FUG | pdb_00003fug

Crystal Structure of the Retinoid X Receptor Ligand Binding Domain Bound to the Synthetic Agonist 3-[4-Hydroxy-3-(3,5,5,8,8-pentamethyl-5,6,7,8-tetrahydronaphthalen-2-yl)-phenyl]acrylic Acid

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	20% PEG 4000, 0.1M TRIS, 1M AMMONIUM ACETATE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.763	α = 90
b = 65.763	β = 90
c = 110.857	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 210		2007-07-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.934	ESRF	ID14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2	31.53	99.9	0.077	0.077		6		17071			21.069

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2	2.11	100		0.377	0.377	2	6.2	2433

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1MVC	2	31.53	17071	17016	882	99.87	0.207	0.207	0.205	0.21	0.241	0.24	RANDOM	19.232

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]
0.62			0.62		-1.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.61
r_dihedral_angle_4_deg	21.69
r_dihedral_angle_3_deg	13.741
r_dihedral_angle_1_deg	4.609
r_scangle_it	2.406
r_scbond_it	1.544
r_angle_refined_deg	1.166
r_mcangle_it	1.069
r_mcbond_it	0.625
r_symmetry_hbond_refined	0.311

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.61
r_dihedral_angle_4_deg	21.69
r_dihedral_angle_3_deg	13.741
r_dihedral_angle_1_deg	4.609
r_scangle_it	2.406
r_scbond_it	1.544
r_angle_refined_deg	1.166
r_mcangle_it	1.069
r_mcbond_it	0.625
r_symmetry_hbond_refined	0.311
r_nbtor_refined	0.3
r_nbd_refined	0.194
r_symmetry_vdw_refined	0.185
r_xyhbond_nbd_refined	0.12
r_chiral_restr	0.085
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1752
Nucleic Acid Atoms
Solvent Atoms	112
Heterogen Atoms	27

Software

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

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.