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Crystal structure of the neurotensin receptor 1 in complex with the small-molecule full agonist cp28a
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 4.5 293.15 100 mM Na acetate
350 mM K citrate tribasic
30% (v/v) PEG400
50 uM cp28a
Crystal Properties Matthews coefficient Solvent content 3.68 66.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.661 α = 90 b = 215.887 β = 90 c = 95.623 γ = 90
Symmetry Space Group C 2 2 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 EIGER X 16M 2023-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0000 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 3.12 107.9 87.8 0.22 0.05 0.99 10.8 25.6 9464
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 3.12 3.47 43.6 4.7 0.97 0.2 1.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3.124 107.9 9464 462 66.14 0.301 0.3002 0.3015 0.322 0.3163 83.853
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] -2.971 1.653 1.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 11.525 r_dihedral_angle_3_deg 10.648 r_dihedral_angle_2_deg 9.129 r_lrange_it 6.714 r_lrange_other 6.714 r_dihedral_angle_1_deg 4.4 r_mcangle_it 2.694 r_mcangle_other 2.694 r_scangle_it 2.344 r_scangle_other 2.343
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 11.525 r_dihedral_angle_3_deg 10.648 r_dihedral_angle_2_deg 9.129 r_lrange_it 6.714 r_lrange_other 6.714 r_dihedral_angle_1_deg 4.4 r_mcangle_it 2.694 r_mcangle_other 2.694 r_scangle_it 2.344 r_scangle_other 2.343 r_mcbond_it 1.503 r_mcbond_other 1.502 r_scbond_it 1.294 r_scbond_other 1.294 r_angle_refined_deg 0.9 r_angle_other_deg 0.294 r_symmetry_xyhbond_nbd_refined 0.229 r_nbd_refined 0.222 r_nbtor_refined 0.178 r_symmetry_nbd_other 0.176 r_nbd_other 0.167 r_symmetry_nbd_refined 0.16 r_xyhbond_nbd_refined 0.086 r_symmetry_nbtor_other 0.072 r_chiral_restr 0.032 r_chiral_restr_other 0.007 r_gen_planes_refined 0.003 r_bond_refined_d 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 3127 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 66
Software Software Software Name Purpose XDS data scaling Aimless data scaling Coot model building REFMAC refinement ISOLDE model building