3VRV

VDR ligand binding domain in complex with 2-Methylidene-26,27-dimethyl-19,24-dinor-1alpha,25-dihydroxyvitamin D3

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	MES-Na, Na-Formate, PEG 4000, Ethyleneglycol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 154.14	α = 90
b = 42.77	β = 95.42
c = 42.12	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	95	CCD	ADSC QUANTUM 210		2010-10-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.000	Photon Factory	AR-NW12A

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	1.9	76.725	94.6	0.047	15.6	3.7	20511	20511

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2	95.1		0.343	0.343	0.4	0.205	2.2	3.7	3019

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.9	29.74	20497	1056	93.95	0.2111	0.2091	0.2482	RANDOM	36.6148

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]
-0.29		-0.06	0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.621
r_dihedral_angle_3_deg	16.978
r_dihedral_angle_4_deg	9.62
r_scangle_it	5.885
r_dihedral_angle_1_deg	5.395
r_scbond_it	3.719
r_mcangle_it	3.288
r_angle_refined_deg	1.87
r_mcbond_it	1.834
r_chiral_restr	0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.621
r_dihedral_angle_3_deg	16.978
r_dihedral_angle_4_deg	9.62
r_scangle_it	5.885
r_dihedral_angle_1_deg	5.395
r_scbond_it	3.719
r_mcangle_it	3.288
r_angle_refined_deg	1.87
r_mcbond_it	1.834
r_chiral_restr	0.13
r_bond_refined_d	0.023
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1974
Nucleic Acid Atoms
Solvent Atoms	107
Heterogen Atoms	31

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
PHASER	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.