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Crystal structure of the neurotensin receptor 1 in complex with the small-molecule inverse agonist SR142948A
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 6.5 293.15 100 mM Bis-Tris
400 mM K citrate
30% (v/v) PEG400
10 uM SR142948A
Crystal Properties Matthews coefficient Solvent content 3.04 59.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 211.924 α = 90 b = 36.845 β = 113.65 c = 90.288 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 2018-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.999998 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.923 28.307 78.2 0.202 0.225 0.097 0.989 4.7 4.7 8671
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.923 3.324 23.9 2.099 2.287 0.895 0.484 1.5 6.4
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 2.923 28.307 8669 440 60.335 0.282 0.2806 0.2819 0.3069 0.3124 52.98
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] 0.476 -0.153 0.692 -0.747
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.45 r_dihedral_angle_3_deg 14.646 r_dihedral_angle_4_deg 11.687 r_lrange_it 5.78 r_lrange_other 5.779 r_dihedral_angle_1_deg 4.225 r_mcangle_it 1.564 r_mcangle_other 1.564 r_angle_refined_deg 1.186 r_scangle_it 1.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.45 r_dihedral_angle_3_deg 14.646 r_dihedral_angle_4_deg 11.687 r_lrange_it 5.78 r_lrange_other 5.779 r_dihedral_angle_1_deg 4.225 r_mcangle_it 1.564 r_mcangle_other 1.564 r_angle_refined_deg 1.186 r_scangle_it 1.135 r_scangle_other 1.134 r_angle_other_deg 1.123 r_mcbond_it 0.863 r_mcbond_other 0.862 r_scbond_it 0.608 r_scbond_other 0.607 r_nbd_refined 0.168 r_nbd_other 0.162 r_nbtor_refined 0.148 r_symmetry_nbd_other 0.147 r_xyhbond_nbd_refined 0.125 r_symmetry_xyhbond_nbd_refined 0.096 r_symmetry_nbtor_other 0.079 r_symmetry_nbd_refined 0.078 r_chiral_restr 0.03 r_gen_planes_refined 0.002 r_bond_refined_d 0.001 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3026 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing