1RK3

crystal structure of the rat vitamin D receptor ligand binding domain complexed with 1,25-dihydroxyvitamin D3 and a synthetic peptide containing the NR2 box of DRIP 205

X-RAY DIFFRACTION

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	295	PEG 4000, MOPS, ammonium citrate, isopropanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 154.726	α = 90
b = 44.154	β = 96.13
c = 42.072	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	CCD	BRUKER PROTEUM R		2002-10-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ENRAF-NONIUS FR591	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	42.44	99	0.052	10.9	5.7	14565	14475		3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.2	2.3	95		0.198	2.7

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 1RJK	2.2	30	14468	14468	727	99.42	0.19303	0.19303	0.19048	0.24255	RANDOM	34.7

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]
-3.19		-0.62	3.31		-0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.111
r_scangle_it	3.998
r_scbond_it	2.438
r_mcangle_it	1.565
r_angle_refined_deg	1.384
r_mcbond_it	0.822
r_nbd_refined	0.208
r_symmetry_vdw_refined	0.171
r_xyhbond_nbd_refined	0.137
r_symmetry_hbond_refined	0.116

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.111
r_scangle_it	3.998
r_scbond_it	2.438
r_mcangle_it	1.565
r_angle_refined_deg	1.384
r_mcbond_it	0.822
r_nbd_refined	0.208
r_symmetry_vdw_refined	0.171
r_xyhbond_nbd_refined	0.137
r_symmetry_hbond_refined	0.116
r_chiral_restr	0.089
r_bond_refined_d	0.016
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1988
Nucleic Acid Atoms
Solvent Atoms	92
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
SAINT	data reduction
LSCALE	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.