7C7V | pdb_00007c7v

Vitamin D3 receptor/lithochoric acid derivative complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ZLC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	0.1 M MOPS-NaOH (pH 7.0), 0.2 M sodium formate, 12% (w/v) PEG4000, and 8% (v/v) ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
1.78	30.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 158.045	α = 90
b = 36.898	β = 96.963
c = 39.486	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	PIXEL	DECTRIS PILATUS 6M		2015-12-09	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)	CC (Half)	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	40	97.4	0.094	0.996	7.1	3.3		15052

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.13			0.63	0.91	1.63

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2ZLC	2	40	15036	762	97.339	0.201	0.1977	0.21	0.2678	0.28	44.663

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]
-5.813		-0.931	3.688		2.284

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.53
r_dihedral_angle_3_deg	16.167
r_dihedral_angle_4_deg	14.415
r_lrange_it	8.286
r_lrange_other	8.284
r_scangle_it	6.577
r_scangle_other	6.575
r_dihedral_angle_1_deg	6.291
r_mcangle_it	5.054
r_mcangle_other	5.052
r_scbond_it	4.439
r_scbond_other	4.436
r_mcbond_it	3.543
r_mcbond_other	3.542
r_angle_refined_deg	1.578
r_angle_other_deg	1.333
r_nbd_other	0.246
r_nbd_refined	0.212
r_symmetry_nbd_other	0.194
r_symmetry_nbd_refined	0.162
r_nbtor_refined	0.161
r_xyhbond_nbd_refined	0.142
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.081
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_symmetry_xyhbond_nbd_other	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1959
Nucleic Acid Atoms
Solvent Atoms	9
Heterogen Atoms	34

Software

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