2Q60

Crystal structure of the ligand binding domain of polyandrocarpa misakiensis rxr in tetramer in absence of ligand

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1XDK	RXR part of PDB ENTRY 1XDK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	0.1M Pipes. 17% Peg 4K. 15mM Sodium chloride. 1mM n-dodecyl B-D-maltoside, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.26	α = 90
b = 96.12	β = 90
c = 151.72	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	MAR CCD 165 mm		2005-03-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.9794	ESRF	BM30A

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	48.224	99.5	0.071	18.51	5.26	27360	27210		-3	55.294

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)
1	2.9	3	98.6		0.409	4.4	5.22	2560

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	RXR part of PDB ENTRY 1XDK	2.9	48.22	27210	27207	1361	100	0.272	0.269	0.325	RANDOM	59.075

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]
-2.9			4.66		-1.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.78
r_dihedral_angle_4_deg	19.825
r_dihedral_angle_3_deg	15.518
r_dihedral_angle_1_deg	5.498
r_angle_refined_deg	1.003
r_angle_other_deg	0.762
r_mcangle_it	0.532
r_scangle_it	0.34
r_mcbond_it	0.291
r_scbond_it	0.2
r_nbd_refined	0.187
r_nbtor_refined	0.168
r_nbd_other	0.162
r_xyhbond_nbd_refined	0.111
r_symmetry_vdw_other	0.106
r_nbtor_other	0.08
r_symmetry_vdw_refined	0.062
r_chiral_restr	0.056
r_mcbond_other	0.02
r_bond_refined_d	0.006
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6081
Nucleic Acid Atoms
Solvent Atoms	175
Heterogen Atoms

Software

Software
Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
XDS	data reduction