3W5R

Crystal structure of complexes of vitamin D receptor ligand binding domain with lithocholic acid derivatives

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	291.5	0.1M 3-(N-morpholino) propanesulfonic acid/sodium hydroxide, 0.1-0.4M sodium formate, 12-22% PEG 4000, 0-10% ethylene glycol , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.5K

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 154.433	α = 90
b = 42.026	β = 96.25
c = 41.514	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	95	CCD	ADSC QUANTUM 4r		2006-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-6A	0.978	Photon Factory	BL-6A

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	2.2	50	99.3	0.058	0.058	26.2	4.3		13707			26.8

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)
1	2.2	2.28	95.9		0.295	0.295	4.4	4	1319

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	PDB ENTRY 1RJK	2.2	40.54	14001	12697	1304	92.7	0.226	0.22	0.276	RANDOM

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]
-20.88		-7.24	29.1		-8.21

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	19.3
c_scangle_it	2.91
c_mcangle_it	2.46
c_scbond_it	2.06
c_mcbond_it	1.46
c_angle_deg	1.2
c_improper_angle_d	0.94
c_bond_d	0.007
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2032
Nucleic Acid Atoms
Solvent Atoms	49
Heterogen Atoms	30

Software

Software
Software Name	Purpose
SERGUI	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing