2ZXZ | pdb_00002zxz

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

X-RAY DIFFRACTION

Starting Model(s)

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

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
1.99	38.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.079	α = 90
b = 64.079	β = 90
c = 110.389	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 315		2007-10-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.00	ESRF	ID29

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	3	50	99.9	0.102	0.102	33.776	12.3	5032	5032			57.611

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)
	3	3.11	100		0.333		12.6	481

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	PDB ENTRY 1MZN	3	10	4831	226	100	0.21	0.21	0.206	0.21	0.278	RANDOM	41.876

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]
0.66			0.66		-1.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.847
r_dihedral_angle_4_deg	22.165
r_dihedral_angle_3_deg	14.445
r_dihedral_angle_1_deg	3.734
r_angle_refined_deg	1.023
r_scangle_it	0.677
r_mcangle_it	0.422
r_scbond_it	0.399
r_nbtor_refined	0.291
r_mcbond_it	0.228

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.847
r_dihedral_angle_4_deg	22.165
r_dihedral_angle_3_deg	14.445
r_dihedral_angle_1_deg	3.734
r_angle_refined_deg	1.023
r_scangle_it	0.677
r_mcangle_it	0.422
r_scbond_it	0.399
r_nbtor_refined	0.291
r_mcbond_it	0.228
r_nbd_refined	0.172
r_symmetry_vdw_refined	0.169
r_xyhbond_nbd_refined	0.109
r_symmetry_hbond_refined	0.107
r_chiral_restr	0.059
r_bond_refined_d	0.006
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1778
Nucleic Acid Atoms
Solvent Atoms	21
Heterogen Atoms	27

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 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.