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Crystal structure of active mu-opioid receptor bound to the agonist BU72
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DKL 4DKL, 3P0G experimental model PDB 3P0G 4DKL, 3P0G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 7.5 293 Reconstituted in 10:1 monoolein:cholesterol mix. Precipitant solution:15-25% PEG300, 100 mM HEPES pH 7.0-7.5, 1% 1,2,3-heptanetriol, 0.5-1.0% Polypropylene glycol P 400, 100-300 mM (NH4)2HPO4
Crystal Properties Matthews coefficient Solvent content 3.54 65.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.43 α = 90 b = 144 β = 90 c = 209.9 γ = 90
Symmetry Space Group I 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 80 PIXEL PSI PILATUS 6M 2014-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.07 43.47 99.8 0.112 0.992 11 8.6 41704 -3 43.71
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.07 2.12 1.536 0.647 1.7
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4DKL, 3P0G 2.07 43.47 1.35 41704 2086 99.8 0.2004 0.1989 0.2291 0.2409 58.4
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 14.26 f_angle_d 0.69 f_chiral_restr 0.0471 f_plane_restr 0.004 f_bond_d 0.0036
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3259 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 131
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XSCALE data scaling PDB_EXTRACT data extraction PHASER phasing XDS data reduction