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Crystal structure of the neurotensin receptor 1 in complex with the small molecule inverse agonist SR48692
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YVR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 293.15 100 mM Bis-Tris
500 mM K citrate
30% (v/v) PEG400
10 uM SR48692
Crystal Properties Matthews coefficient Solvent content 3.11 60.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 212.98 α = 90 b = 37.15 β = 113.6 c = 91.21 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 100 PIXEL DECTRIS EIGER X 16M 2018-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.999879 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 2.639 28.569 85.4 0.123 0.063 0.993 5.7 4.5 12018
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.639 2.965 1.206 0.612 0.512 1.2
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 6YVR 2.639 28.567 12008 605 60.509 0.268 0.266 0.2677 0.3098 0.3131 67.498
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] 1.428 1.514 -2.161 -0.427
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.971 r_dihedral_angle_4_deg 18.391 r_dihedral_angle_3_deg 14.939 r_lrange_it 5.305 r_lrange_other 5.305 r_dihedral_angle_1_deg 4.608 r_mcangle_it 1.341 r_mcangle_other 1.341 r_angle_refined_deg 1.197 r_angle_other_deg 1.123
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.971 r_dihedral_angle_4_deg 18.391 r_dihedral_angle_3_deg 14.939 r_lrange_it 5.305 r_lrange_other 5.305 r_dihedral_angle_1_deg 4.608 r_mcangle_it 1.341 r_mcangle_other 1.341 r_angle_refined_deg 1.197 r_angle_other_deg 1.123 r_scangle_it 1.106 r_scangle_other 1.106 r_mcbond_it 0.75 r_mcbond_other 0.75 r_scbond_it 0.6 r_scbond_other 0.6 r_nbd_refined 0.175 r_symmetry_nbd_other 0.16 r_nbtor_refined 0.151 r_xyhbond_nbd_refined 0.15 r_nbd_other 0.12 r_symmetry_nbd_refined 0.103 r_symmetry_xyhbond_nbd_refined 0.095 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.035 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3117 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing