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Crystal structure of the neurotensin receptor 1 in complex with the small-molecule full agonist SRI-9829
Serial Crystallography (SX)
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 6.8 293.15 100 mM HEPES
370-520 mM Na citrate
32% (v/v) PEG400
10 uM SRI-9829
Crystal Properties Matthews coefficient Solvent content 3.51 64.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.665 α = 90 b = 213.971 β = 90 c = 94.052 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 2018-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.999998 SLS X06SA
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 fixed target
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 2.803 29.595 90.4 0.208 0.232 0.099 0.982 5.1 5.2 13189
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 2.803 3.127 1.866 2.05 0.82 0.32 1.4
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 2.803 29.595 13154 659 67.623 0.278 0.277 0.2779 0.2986 0.3022 65.825
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] 0.576 -0.928 0.353
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.118 r_dihedral_angle_3_deg 13.553 r_dihedral_angle_4_deg 11.921 r_lrange_other 5.866 r_lrange_it 5.863 r_dihedral_angle_1_deg 4.25 r_mcangle_it 1.835 r_mcangle_other 1.835 r_scangle_it 1.29 r_scangle_other 1.289
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.118 r_dihedral_angle_3_deg 13.553 r_dihedral_angle_4_deg 11.921 r_lrange_other 5.866 r_lrange_it 5.863 r_dihedral_angle_1_deg 4.25 r_mcangle_it 1.835 r_mcangle_other 1.835 r_scangle_it 1.29 r_scangle_other 1.289 r_angle_refined_deg 1.169 r_angle_other_deg 1.116 r_mcbond_it 1.008 r_mcbond_other 1.007 r_scbond_it 0.683 r_scbond_other 0.683 r_nbd_refined 0.174 r_nbtor_refined 0.152 r_symmetry_nbd_other 0.15 r_symmetry_xyhbond_nbd_refined 0.149 r_xyhbond_nbd_refined 0.133 r_nbd_other 0.11 r_symmetry_nbd_refined 0.109 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.031 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 3302 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing