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PXR in complex with P2X4 inhibitor compound 25
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 0.1902 0.22611 0.2289 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
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