7VQP

Vitamin D receptor complexed with a lithocholic acid derivative

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	297	0.1 M MOPS-NaOH, 0.1-0.4 M sodium formate, 12-22% (w/v) PEG4000, 5% (v/v) ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
1.86	34.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 157.805	α = 90
b = 37.581	β = 98.59
c = 40.913	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	PIXEL	DECTRIS EIGER X 16M		2021-02-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	0.9800	Photon Factory	BL-17A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	CC (Half)	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	1.94	40	98.4	0.056	0.999	8.6	3.4		17530

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.94	2.01	98.2		0.567	0.876	1.7	3.5

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-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2ZLC	1.94	40	17523	848	98.058	0.209	0.207	0.2424	33.815

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]
0.109		-0.06	-0.11		0.018

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.268
r_dihedral_angle_4_deg	16.235
r_dihedral_angle_3_deg	15.375
r_lrange_it	6.69
r_lrange_other	6.688
r_dihedral_angle_1_deg	5.581
r_scangle_it	5.176
r_scangle_other	5.174
r_mcangle_it	3.692
r_mcangle_other	3.691
r_scbond_it	3.405
r_scbond_other	3.401
r_mcbond_it	2.564
r_mcbond_other	2.562
r_angle_refined_deg	1.514
r_angle_other_deg	1.306
r_symmetry_nbd_refined	0.209
r_nbd_refined	0.208
r_symmetry_nbd_other	0.165
r_nbd_other	0.162
r_nbtor_refined	0.16
r_xyhbond_nbd_refined	0.146
r_symmetry_xyhbond_nbd_refined	0.112
r_chiral_restr	0.077
r_symmetry_nbtor_other	0.077
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1927
Nucleic Acid Atoms
Solvent Atoms	10
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing