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Re-refined model of active mu-opioid receptor (PDB 5c1m) as an adduct with BU72
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5C1M 5C1M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 7.5 293 Reconstituted in 10:1 monoolein:cholesterol mix, precipitant: 15-25% PEG300, 100 mM HEPES, pH 7.0-7.5, 1% 1,2,3-heptanetriol, 0.5-1.0% polypropylene glycol P400, 100-300 mM ammonium phosphate dibasic
Crystal Properties Matthews coefficient Solvent content 3.59 65.78
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) 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 1.8 43.5 99.5 0.142 7.51 8.5 63134
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 95 1.4451
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5C1M 2.1 43.5 37971 1999 99.8 0.19319 0.1915 0.2112 0.22548 0.2376 RANDOM 57.315
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] -1.02 3.63 -2.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.779 r_dihedral_angle_4_deg 20.43 r_dihedral_angle_3_deg 16.258 r_long_range_B_refined 9.553 r_long_range_B_other 9.553 r_scangle_other 6.634 r_dihedral_angle_1_deg 6.624 r_scbond_it 4.627 r_scbond_other 4.626 r_mcangle_it 4.204
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.779 r_dihedral_angle_4_deg 20.43 r_dihedral_angle_3_deg 16.258 r_long_range_B_refined 9.553 r_long_range_B_other 9.553 r_scangle_other 6.634 r_dihedral_angle_1_deg 6.624 r_scbond_it 4.627 r_scbond_other 4.626 r_mcangle_it 4.204 r_mcangle_other 4.203 r_mcbond_it 2.914 r_mcbond_other 2.911 r_angle_refined_deg 1.873 r_angle_other_deg 1.359 r_chiral_restr 0.146 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3308 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 99
Software Software Software Name Purpose REFMAC refinement