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Crystal structure of the active delta opioid receptor in complex with the small molecule agonist DPI-287
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4N6H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 6 293 32-35% PEG400, 100-110 mM potassium citrate tribasic monohydrate and 100 mM MES pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.69 54.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.084 α = 90 b = 142.101 β = 90 c = 157.491 γ = 90
Symmetry Space Group P 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 293 PIXEL DECTRIS PILATUS 6M 2018-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.00 SPring-8 BL41XU
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 3.3 49.24 94.5 0.114 8.67 7 16342
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 3.3 3.39 0.889
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 4n6h 3.3 49.24 16341 781 94.5 0.246 0.245 0.2557 0.269 0.2813 RANDOM 133.77
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] -23.3867 23.348 0.0387
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 3.02 t_omega_torsion 2.2 t_angle_deg 1.05 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 3.02 t_omega_torsion 2.2 t_angle_deg 1.05 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5646 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 72
Software Software Software Name Purpose PHASER phasing BUSTER refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling