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PXR IN COMPLEX WITH THROMBIN INHIBITOR COMPOUND 17
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 25 MILLIMOLAR COMPOUND 17 (FROM 500 MILLIMOLAR STOCK IN DMSO) for 24 hours at 277 K, MIXED WITH 1 MICROLITER OF RESERVOIR (100 MILLIMOLAR IMIDAZOLE PH 8.0, 20 % (V/V) MPD). CRYO BUFFER 100 MILLIMOLAR IMIDAZOLE PH 8.0, 30 % (V/V) MPD
Crystal Properties Matthews coefficient Solvent content 2.56 51.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.356 α = 90 b = 88.964 β = 90 c = 105.658 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 MARMOSAIC 225 mm CCD 2010-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 1.85 44.48 97.9 0.053 0.059 0.999 17.15 5.07 67925 39.61
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.96 98.7 0.878 0.977 0.668 1.82 5
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 1.85 44.48 65823 2101 97.9 0.17276 0.17192 0.1806 0.19932 0.2111 RANDOM 41.918
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] -0.6 0.25 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.873 r_dihedral_angle_3_deg 14.978 r_dihedral_angle_4_deg 14.137 r_long_range_B_refined 9.443 r_long_range_B_other 9.404 r_scangle_other 6.625 r_dihedral_angle_1_deg 5.192 r_mcangle_it 4.67 r_mcangle_other 4.669 r_scbond_it 4.209
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.873 r_dihedral_angle_3_deg 14.978 r_dihedral_angle_4_deg 14.137 r_long_range_B_refined 9.443 r_long_range_B_other 9.404 r_scangle_other 6.625 r_dihedral_angle_1_deg 5.192 r_mcangle_it 4.67 r_mcangle_other 4.669 r_scbond_it 4.209 r_scbond_other 4.208 r_mcbond_it 3.081 r_mcbond_other 3.081 r_angle_refined_deg 1.308 r_angle_other_deg 1.265 r_chiral_restr 0.074 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 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 4847 Nucleic Acid Atoms Solvent Atoms 360 Heterogen Atoms 89
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing