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Structure of nanobody-stabilized angiotensin II type 1 receptor bound to S1I8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YAY 4YAY, 3P0G experimental model PDB 3P0G 4YAY, 3P0G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 8 293.15 Protein was reconstituted with a 10:1 (w:w) mix of monoolein and cholesterol. Crystals were grown in cubic phase sandwich plates with using 100 mM Tris pH 8.0, 15-25 mM MgCl2, and 28-29% PEG 300
Crystal Properties Matthews coefficient Solvent content 2.08 41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.682 α = 90 b = 227.796 β = 90 c = 41.5 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS EIGER X 16M 2018-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.9 45.6 98.5 0.41 0.962 2.1 3.6 29111
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3.08 99.3 1.457 1.697 0.562 0.9 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4YAY, 3P0G 2.901 43.618 1.33 28820 1942 97.22 0.3082 0.3045 0.309 0.3593 0.3127
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.681 f_angle_d 0.912 f_chiral_restr 0.044 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7744 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 110
Software Software Software Name Purpose PHENIX refinement JBluIce-EPICS data collection Coot model building PHASER phasing XDS data reduction Aimless data scaling