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Crystal structure of the neurotensin receptor 1 (NTSR1-H4bmx) in complex with the small molecule inverse agonist SR48692
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 293.15 100 mM Na citrate
225-460 mM ammonium nitrate
30-32% (v/v) PEG400
1 uM SR48692
Crystal Properties Matthews coefficient Solvent content 2.43 49.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.518 α = 90 b = 77.727 β = 90 c = 158.394 γ = 90
Symmetry Space Group P 21 21 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 2019-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.000009 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 2.707 29.353 90.6 0.525 0.564 0.198 0.964 4.3 7.3 10475
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 2.707 3.029 4.678 4.929 1.504 0.294 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 2.707 29.353 10474 552 68.408 0.274 0.2727 0.2754 0.2889 0.2953 38.575
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] 0.315 1.193 -1.508
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.948 r_dihedral_angle_3_deg 15.324 r_dihedral_angle_4_deg 12.63 r_dihedral_angle_1_deg 3.868 r_lrange_other 3.389 r_lrange_it 3.387 r_angle_refined_deg 1.165 r_angle_other_deg 1.08 r_mcangle_it 0.976 r_mcangle_other 0.976
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.948 r_dihedral_angle_3_deg 15.324 r_dihedral_angle_4_deg 12.63 r_dihedral_angle_1_deg 3.868 r_lrange_other 3.389 r_lrange_it 3.387 r_angle_refined_deg 1.165 r_angle_other_deg 1.08 r_mcangle_it 0.976 r_mcangle_other 0.976 r_scangle_it 0.572 r_scangle_other 0.572 r_mcbond_it 0.523 r_mcbond_other 0.523 r_scbond_it 0.284 r_scbond_other 0.284 r_nbd_refined 0.167 r_nbtor_refined 0.152 r_symmetry_nbd_other 0.145 r_nbd_other 0.135 r_symmetry_xyhbond_nbd_other 0.126 r_symmetry_nbd_refined 0.117 r_xyhbond_nbd_refined 0.115 r_symmetry_xyhbond_nbd_refined 0.091 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.032 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 3288 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing