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Crystal structure of the neurotensin receptor 1 in complex with the small-molecule full agonist cp30a
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 5.6 293.15 100 mM Na cacodylate
350 mM K citrate tribasic
30% (v/v) PEG400
50 uM cp30a
Crystal Properties Matthews coefficient Solvent content 3.71 66.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.888 α = 90 b = 216.06 β = 90 c = 96.014 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 2023-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97626 PETRA III, EMBL c/o DESY P13 (MX1)
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 3.1 71.6 91 1 0.25 0.97 8.5 15.8 11602
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 3.1 3.39 9.86 2.44 0.71 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 3.112 71.6 11602 571 79.569 0.313 0.3121 0.3007 0.3249 0.3031 26.899
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] 0.159 1.966 -2.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 12.424 r_dihedral_angle_3_deg 10.709 r_lrange_it 5.658 r_lrange_other 5.658 r_dihedral_angle_1_deg 4.776 r_dihedral_angle_2_deg 3.673 r_mcangle_it 2.449 r_mcangle_other 2.448 r_scangle_it 1.654 r_scangle_other 1.654
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 12.424 r_dihedral_angle_3_deg 10.709 r_lrange_it 5.658 r_lrange_other 5.658 r_dihedral_angle_1_deg 4.776 r_dihedral_angle_2_deg 3.673 r_mcangle_it 2.449 r_mcangle_other 2.448 r_scangle_it 1.654 r_scangle_other 1.654 r_mcbond_it 1.333 r_mcbond_other 1.333 r_angle_refined_deg 1.012 r_scbond_it 0.868 r_scbond_other 0.868 r_angle_other_deg 0.373 r_symmetry_nbd_refined 0.268 r_symmetry_xyhbond_nbd_refined 0.24 r_nbd_refined 0.228 r_symmetry_nbd_other 0.194 r_nbtor_refined 0.186 r_nbd_other 0.181 r_xyhbond_nbd_refined 0.129 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.044 r_gen_planes_refined 0.006 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3304 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement XDS data scaling Aimless data scaling ISOLDE model building XDS data reduction PHASER phasing