1UPV | pdb_00001upv

Crystal structure of the human Liver X receptor beta ligand binding domain in complex with a synthetic agonist

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		RESERVOIR: 25% MPD, 10% PEG4K, 100 MM HEPES PH 7.5, 10 MM D PROTEIN: 4-8 MG/ML IN 20 MM TRIS PH 8.0, 100 MM NACL, 10 MM

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 141.8	α = 90
b = 43.2	β = 105.8
c = 51.8	γ = 90

Symmetry
Space Group	C 1 2 1

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	MARRESEARCH	MIRRORS	2002-10-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA		SLS	X06SA

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	2.1	30	83.3	0.093	6.4	2.6		15111

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	2.1	2.18	71.3		0.317	2	2.2

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-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1FCY	2.1	20	14163	755	83.5	0.215	0.274	RANDOM	16.85

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]
1.01		2.34	-2.27		2.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	4.769
r_scangle_it	3.378
r_scbond_it	1.889
r_angle_refined_deg	1.213
r_mcangle_it	1.057
r_mcbond_it	0.52
r_symmetry_vdw_refined	0.245
r_nbd_refined	0.221
r_symmetry_hbond_refined	0.192
r_xyhbond_nbd_refined	0.166
r_chiral_restr	0.093
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1875
Nucleic Acid Atoms
Solvent Atoms	97
Heterogen Atoms	31

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing