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Structure of the N/OFQ Opioid Receptor in Complex with a Peptide Mimetic
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DJH pdb entry 4DJH,1M6T experimental model PDB 1M6T pdb entry 4DJH,1M6T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Lipidic Cubic Phase (LCP) 6.4 293 25-30% (v/v) PEG 400,
100 to 200 mM potassium sodium tartrate tetrahydrate,
100 mM BIS-TRIS propane pH 6.4 , Lipidic Cubic Phase (LCP), temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.38 48.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.106 α = 90 b = 170.939 β = 103.14 c = 65.353 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD DOUBLE CRYSTAL MONOCHROMATOR AND K-B PAIR OF BIOMORPH MIRRORS FOR VERTICAL AND HORIZONTAL FOCUSING 2011-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0330 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 3 50 93.3 0.19 8.5 2.9 16545 16545 58.79
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 3.11 79.5 0.66 2 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 4DJH,1M6T 3.013 32.019 1.34 16506 16506 845 93.12 0.2505 0.2484 0.2884 0.3 random
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] -6.6868 -1.7825 -12.997 -11.4978
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.967 f_angle_d 0.563 f_chiral_restr 0.031 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5007 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 115
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling