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Crystal structure of the neurotensin receptor 1 in complex with the peptide full agonist NTS8-13
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XEE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.4 277.1 50mM glycine
1M NaCl
8.3% (w/v) PEG4000
Cryoprotectant solution contained:
50mM glycine pH 9.4
1M NaCl
100nM NTS8-13
15% (v/v) PEG600
15% (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 4.49 72.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.886 α = 90 b = 114.001 β = 90 c = 195.424 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 2017-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.000031 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 2.458 29.633 93.9 0.094 0.098 0.028 0.999 15.2 12 59974
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 2.458 2.647 1.711 1.801 0.555 0.597 1.6
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4XEE 2.458 29.633 59974 2958 81.168 0.229 0.2284 0.2375 0.2292 70.765
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] -0.652 -0.561 1.213
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.931 r_dihedral_angle_4_deg 21.694 r_dihedral_angle_3_deg 14.168 r_lrange_it 7.736 r_lrange_other 7.736 r_scangle_it 6.42 r_scangle_other 6.42 r_dihedral_angle_1_deg 5.345 r_mcangle_it 5.025 r_mcangle_other 5.025
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.931 r_dihedral_angle_4_deg 21.694 r_dihedral_angle_3_deg 14.168 r_lrange_it 7.736 r_lrange_other 7.736 r_scangle_it 6.42 r_scangle_other 6.42 r_dihedral_angle_1_deg 5.345 r_mcangle_it 5.025 r_mcangle_other 5.025 r_scbond_it 4.465 r_scbond_other 4.465 r_mcbond_it 3.518 r_mcbond_other 3.517 r_angle_refined_deg 1.265 r_angle_other_deg 1.193 r_nbd_refined 0.189 r_symmetry_nbd_other 0.167 r_nbtor_refined 0.154 r_nbd_other 0.154 r_xyhbond_nbd_refined 0.15 r_symmetry_xyhbond_nbd_refined 0.099 r_symmetry_nbd_refined 0.089 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.054 r_ncsr_local_group_1 0.034 r_bond_refined_d 0.004 r_gen_planes_refined 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 7134 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 168
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing