3X36

Crystal structure of the human vitamin D receptor ligand binding domain complexed with 7,8-cis-1a,25-Dihydroxy-19-norvitamin D3

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	293	0.1M MES, pH6.5, 1.2-1.6M ammonium sulfate, VAPOR DIFFUSION, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.819	α = 90
b = 51.27	β = 90
c = 132.166	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 315r		2013-07-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.95370	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.93	47.8	78.2					2	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.93	2.03	24.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	1.93	42.48	17506	939	78.01	0.17918	0.1769	0.22129	RANDOM	18.734

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]
-0.55			-0.38		0.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.625
r_dihedral_angle_4_deg	19.651
r_dihedral_angle_3_deg	17.272
r_dihedral_angle_1_deg	6.946
r_angle_refined_deg	2.116
r_angle_other_deg	1.004
r_chiral_restr	0.129
r_bond_refined_d	0.018
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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	2022
Nucleic Acid Atoms
Solvent Atoms	131
Heterogen Atoms	29

Software

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