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Crystal structure of a peptidergic GPCR in complex with a small synthetic G protein-biased agonist
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VBL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 4.75 293 25 to 35 % polyethylene glycol (PEG) 400, 100 mM sodium citrate, pH 4.75, and 150 mM of ammonium phosphate or ammonium acetate
Crystal Properties Matthews coefficient Solvent content 2.51 51.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.823 α = 90 b = 153.948 β = 90 c = 111.646 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 PILATUS3 6M 2019-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96863 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.58 76.97 90.1 0.145 0.923 7.1 14.8 9698
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.58 2.929 0.497 1.5
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.584 76.97 9705 481 53.4 0.2344 0.2321 0.2754 0.2777 RANDOM 65.57
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] -6.7372 -3.5527 10.2899
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 21.77 t_omega_torsion 2.55 t_angle_deg 0.92 t_bond_d 0.008 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3024 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 105
Software Software Software Name Purpose BUSTER refinement Coot model building GDA data collection XDS data reduction STARANISO data scaling PHASER phasing