2O4R | pdb_00002o4r

Crystal Structure of Rat Vitamin D Receptor Ligand Binding Domain Complexed with VitIII 17-20E and 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	macroseeding in batch	7	295	PEG 4000, MOPS, Ammonium Citrate, Isopropanol, pH 7.0, macroseeding in batch, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2	38.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 154	α = 90
b = 43	β = 96
c = 42	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	Montel Optics	2005-11-30		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE

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	1.98	42.5	99.8	0.0447	22.77	7.03	19228	19195		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)
	1.98	2.08	99.6		0.186	4.49	3.61	2611

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	pdb entry 1RJK	1.98	30	18621	18621	956	96.4	0.189	0.186	0.18	0.24	0.24	RANDOM	26.771

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]
-2.57		-0.19	2.72		-0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.033
r_dihedral_angle_4_deg	20.133
r_dihedral_angle_3_deg	15.015
r_dihedral_angle_1_deg	4.879
r_scangle_it	3.865
r_scbond_it	2.436
r_mcangle_it	1.579
r_angle_refined_deg	1.467
r_mcbond_it	0.932
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.033
r_dihedral_angle_4_deg	20.133
r_dihedral_angle_3_deg	15.015
r_dihedral_angle_1_deg	4.879
r_scangle_it	3.865
r_scbond_it	2.436
r_mcangle_it	1.579
r_angle_refined_deg	1.467
r_mcbond_it	0.932
r_nbtor_refined	0.308
r_nbd_refined	0.21
r_symmetry_vdw_refined	0.197
r_symmetry_hbond_refined	0.161
r_xyhbond_nbd_refined	0.137
r_chiral_restr	0.084
r_bond_refined_d	0.014
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1999
Nucleic Acid Atoms
Solvent Atoms	166
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
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.