6HTY | pdb_00006hty

PXR in complex with P2X4 inhibitor compound 25

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	277	1 microliter protein at 12.1 mg/ml (in 20 millimolar Tris pH 7.8, 250 millimolar NaCl, 2.5 millimolar EDTA, 5% (v/v) glycerol, 5 mM DTT), preincubated with 10 millimolar compound 15 (from 200 millimolar stock in DMSO), mixed with 1 microliter of reservoir (100 mM imidazole pH 8.0, 17 % (v/v) MPD). Crystals additionally soaked in 20 millimolar compound 15 prior to data collection. cryo buffer 34% (v/v) MPD supplemented with 20 millimolar compound 15

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.417	α = 90
b = 88.616	β = 90
c = 104.929	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	PIXEL	DECTRIS PILATUS 6M		2014-10-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	1.040432	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	2.22	45.15	99.3	0.065	0.999	15.4	5		39804			57.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.22	2.35	98.6		0.847	0.707	1.7	4.9

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	FOURIER SYNTHESIS	THROUGHOUT	3HVL	2.22	45.15	37812	1991	99.34	0.18674	0.1847	0.19	0.22611	0.23	RANDOM	69.232

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]
-1.43			1.01		0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.91
r_dihedral_angle_3_deg	16.924
r_dihedral_angle_4_deg	16.542
r_long_range_B_other	12.052
r_long_range_B_refined	12.042
r_scangle_other	8.709
r_mcangle_it	7.198
r_mcangle_other	7.198
r_scbond_it	5.786
r_scbond_other	5.786
r_dihedral_angle_1_deg	5.4
r_mcbond_it	4.683
r_mcbond_other	4.677
r_angle_refined_deg	1.42
r_angle_other_deg	0.97
r_chiral_restr	0.08
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001
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	4869
Nucleic Acid Atoms
Solvent Atoms	148
Heterogen Atoms	55

Software

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