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Molecular mechanism of biased signaling at the kappa opioid receptor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6B73
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 6.7 293 40-200 mM magnesium sulfate hydrate, 100 mM sodium citrate tribasic dehydrate, 10 mM Manganese (II) chloride tetrahydrate
28-30% PEG400
Crystal Properties Matthews coefficient Solvent content 3.39 63.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.75 α = 90 b = 76.53 β = 90 c = 154.46 γ = 90
Symmetry Space Group P 2 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 83 PIXEL DECTRIS EIGER X 16M 2018-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0330 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3.3 38.38 94.5 0.99 5.2 6.4 40881 125.38
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 3.3 3.56 0.5
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 6B73 3.3 37.14 1.33 12420 1244 94.19 0.2899 0.2851 0.2861 0.3352 0.3377 130.81
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 7.6089 f_angle_d 0.8204 f_chiral_restr 0.0446 f_plane_restr 0.0046 f_bond_d 0.0045
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3351 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 35
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction XDS data scaling PHASER phasing