1XIU | pdb_00001xiu

Crystal structure of the agonist-bound ligand-binding domain of Biomphalaria glabrata RXR

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	HEPES, sodium formate, sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.17	61.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.1	α = 90
b = 87.1	β = 90
c = 320.4	γ = 120

Symmetry
Space Group	P 61 2 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		2003-05-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.976	ESRF	ID29

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	2.5	25		0.094	19.5	15.6		25831	2	2

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	2.5	2.65	99.1		0.54	5.98	15.8

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 (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	PDB ENTRY 1FBY	2.5	24.4	24537	24538	1292	100	0.1958	0.19326	0.19	0.24332	0.24	RANDOM	46.191

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]
2.07	1.03		2.07		-3.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.313
r_dihedral_angle_4_deg	27.667
r_dihedral_angle_3_deg	21.767
r_dihedral_angle_1_deg	7.149
r_scangle_it	5.974
r_scbond_it	3.824
r_angle_refined_deg	2.589
r_mcangle_it	2.31
r_mcbond_it	1.4
r_nbtor_refined	0.34
r_symmetry_vdw_refined	0.297
r_nbd_refined	0.267
r_xyhbond_nbd_refined	0.165
r_chiral_restr	0.162
r_symmetry_hbond_refined	0.147
r_bond_refined_d	0.029
r_gen_planes_refined	0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3691
Nucleic Acid Atoms
Solvent Atoms	47
Heterogen Atoms	44

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing