1RJK

crystal structure of the rat vitamin D receptor ligand binding domain complexed with 2MD 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	1DB1	PDB entry 1DB1

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
2.01	38.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 154.6	α = 90
b = 43.292	β = 96.07
c = 41.848	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		2002-10-27	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	1.99	33.07	99	0.051	10.8	4.9	19031	18940		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)
	1.99	2.08	96		0.161	3.5

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1DB1	1.99	30	18937	18937	977	99.54	0.18814	0.18814	0.18502	0.24433	RANDOM	30.927

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]
-2.94		-0.48	3.45		-0.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	4.895
r_scangle_it	4.184
r_scbond_it	2.573
r_mcangle_it	1.637
r_angle_refined_deg	1.394
r_mcbond_it	0.87
r_nbd_refined	0.206
r_symmetry_vdw_refined	0.185
r_xyhbond_nbd_refined	0.133
r_chiral_restr	0.089

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	4.895
r_scangle_it	4.184
r_scbond_it	2.573
r_mcangle_it	1.637
r_angle_refined_deg	1.394
r_mcbond_it	0.87
r_nbd_refined	0.206
r_symmetry_vdw_refined	0.185
r_xyhbond_nbd_refined	0.133
r_chiral_restr	0.089
r_symmetry_hbond_refined	0.089
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1990
Nucleic Acid Atoms
Solvent Atoms	131
Heterogen Atoms	30

Software

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

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.