8IQT

Crystal structure of the human vitamin D receptor ligand binding domain complexed with (23R)-F-25(OH)D3

X-RAY DIFFRACTION

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Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.723	α = 90
b = 51.363	β = 90
c = 132.102	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	PIXEL	DECTRIS PILATUS 6M		2022-10-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1.000	SPring-8	BL45XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.745	47.9	98.8	0.842	13.67	1.37		59041

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.85			0.788

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.745	47.872	31416	1559	98.83	0.183	0.1816	0.2071	26.009

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]
-0.005			-0.001		0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.712
r_dihedral_angle_3_deg	14.548
r_dihedral_angle_2_deg	8
r_lrange_it	7.139
r_lrange_other	7.129
r_scangle_it	6.254
r_scangle_other	6.252
r_dihedral_angle_1_deg	5.29
r_scbond_it	4.099
r_scbond_other	4.097
r_mcangle_other	3.424
r_mcangle_it	3.42
r_mcbond_it	2.52
r_mcbond_other	2.417
r_angle_refined_deg	1.729
r_angle_other_deg	0.571
r_nbd_refined	0.24
r_nbd_other	0.195
r_nbtor_refined	0.181
r_symmetry_nbd_refined	0.181
r_symmetry_nbd_other	0.179
r_xyhbond_nbd_refined	0.131
r_symmetry_xyhbond_nbd_refined	0.131
r_chiral_restr	0.086
r_symmetry_nbtor_other	0.073
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_gen_planes_other	0.006
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2023
Nucleic Acid Atoms
Solvent Atoms	107
Heterogen Atoms	30

Software

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