3A2I

Crystal structure of the human vitamin D receptor (H305F) ligand binding domain complexed with TEI-9647

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.1M MES, pH 6.5, 1.2-1.6M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.796	α = 90
b = 51.365	β = 90
c = 131.773	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	ADSC QUANTUM 210		2007-10-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.000	Photon Factory	AR-NW12A

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	3.25	50	99.9	0.162	14	3.8		5094	2	1

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)
	3.25	3.37	100		0.349	5.06	3.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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 1DB1	3.27	40.52	3	5094	4818	233	99.59	0.22102	0.21844	0.27578	RANDOM	20.392

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]
-0.02			0.03		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.361
r_dihedral_angle_3_deg	15.857
r_dihedral_angle_4_deg	14.589
r_dihedral_angle_1_deg	4.088
r_angle_refined_deg	1.103
r_scangle_it	0.814
r_mcangle_it	0.579
r_scbond_it	0.468
r_mcbond_it	0.325
r_nbtor_refined	0.296
r_nbd_refined	0.181
r_symmetry_vdw_refined	0.147
r_xyhbond_nbd_refined	0.095
r_symmetry_hbond_refined	0.08
r_chiral_restr	0.063
r_bond_refined_d	0.006
r_gen_planes_refined	0.002
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	2014
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	31

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing