5XZH | pdb_00005xzh

Vitamin D receptor with a synthetic ligand ADRO2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3W5P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.1M MOPS/NaOH, 0.2M sodium formate, 14-18%(w/v) PEG4000, 8% (v/v) ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 153.665	α = 90
b = 41.763	β = 95.58
c = 42.01	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 270		2015-06-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	0.98	Photon Factory	BL-17A

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	50	99.2	0.078	7.6	3.2		18042

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	2	2.07	99.4		0.685	1.3	3.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	3W5P	2	50.01	17148	901	99.14	0.19683	0.19432	0.2	0.24338	0.24	RANDOM	50.249

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]
-4.09		-2.36	2.07		2.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.492
r_dihedral_angle_4_deg	20.11
r_dihedral_angle_3_deg	17.532
r_long_range_B_other	9.1
r_long_range_B_refined	9.077
r_scangle_other	7.357
r_dihedral_angle_1_deg	5.95
r_mcangle_other	5.718
r_mcangle_it	5.712
r_scbond_it	4.943
r_scbond_other	4.941
r_mcbond_it	4.045
r_mcbond_other	4.02
r_angle_refined_deg	1.897
r_angle_other_deg	1.061
r_chiral_restr	0.103
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_gen_planes_other	0.004
r_bond_other_d	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2004
Nucleic Acid Atoms
Solvent Atoms	12
Heterogen Atoms	38

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing