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Crystal structure of the active delta opioid receptor in complex with the peptide agonist KGCHM07
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 27-32% PEG400, 100-120 mM potassium citrate tribasic monohydrate and 100 mM MES pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.68 54.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.96 α = 90 b = 140.88 β = 90 c = 158.64 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 2018-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.000 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 2.8 49.51 93.2 0.085 11.9 6.4 26051
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 2.8 2.87 0.804
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 2.8 49.51 26050 1269 93.2 0.247 0.246 0.2508 0.282 0.2939 RANDOM 115.43
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] -19.3644 19.4171 -0.0527
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.09 t_omega_torsion 2.43 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 19.09 t_omega_torsion 2.43 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 5717 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 252
Software Software Software Name Purpose PHASER phasing BUSTER refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling