3A40 | pdb_00003a40

Crystal structure of the human VDR ligand binding domain bound to the synthetic agonist compound 2alpha-methyl-AMCR277B(C23R)

X-RAY DIFFRACTION

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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, SITTING DROP	6	277	10mM Tris, 100mM NaCl, 1nM TCEP, 0.05M Mes, 0.7M ammonium sulfate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.969	α = 90
b = 51.496	β = 90
c = 131.91	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	CCD	ADSC QUANTUM 315r		2008-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.975531	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.45	50	96	0.053	0.053	22.5	2.4	55357	53143			15.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.5	97.5		0.317	0.317	2.6	2.4	5293

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1DB1	1.45	18.5	55357	50391	2712	96.06	0.16216	0.16038	0.16	0.19556	0.2	RANDOM	18.189

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]
-0.59			-0.12		0.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.664
r_dihedral_angle_4_deg	13.869
r_dihedral_angle_3_deg	10.838
r_dihedral_angle_1_deg	4.296
r_scangle_it	3.145
r_scbond_it	2.932
r_sphericity_free	2.807
r_rigid_bond_restr	2.72
r_sphericity_bonded	2.559
r_mcangle_it	1.349
r_angle_refined_deg	1.29
r_mcbond_it	0.803
r_nbtor_refined	0.308
r_nbd_refined	0.206
r_symmetry_hbond_refined	0.176
r_symmetry_vdw_refined	0.157
r_xyhbond_nbd_refined	0.128
r_chiral_restr	0.074
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2026
Nucleic Acid Atoms
Solvent Atoms	458
Heterogen Atoms	43

Software

Software
Software Name	Purpose
REFMAC	refinement
MxCuBE	data collection
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing