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1.8 A Structure of the human delta opioid 7TM receptor (PSI Community Target)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EJ4 PDB ENTRY 4EJ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LCP 293 31-34% (v/v) PEG 400, 0.095 to 0.12 M K/Na tartrate, 5% (v/v) ethylene glycol, 100 mM MES buffer at pH 6.1-6.2, LCP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.76 55.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.23 α = 90 b = 72.851 β = 107.48 c = 84.408 γ = 90
Symmetry Space Group C 1 2 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 mirrors 2013-04-20 M SINGLE WAVELENGTH 2 1 CCD MARMOSAIC 300 mm CCD mirrors 2013-06-16
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 1.8 40 98.5 0.104 16.4 4.5 45488
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 1.86 98.5 0.822 2.3 4.3
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 PDB ENTRY 4EJ4 1.8 29.7 43157 2303 98.26 0.17271 0.17175 0.1833 0.19028 0.2006 RANDOM 39.313
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] 2.4 0.03 -0.41 -1.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.636 r_dihedral_angle_4_deg 16.747 r_dihedral_angle_3_deg 12.935 r_dihedral_angle_1_deg 4.852 r_angle_refined_deg 1.419 r_angle_other_deg 0.851 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.636 r_dihedral_angle_4_deg 16.747 r_dihedral_angle_3_deg 12.935 r_dihedral_angle_1_deg 4.852 r_angle_refined_deg 1.419 r_angle_other_deg 0.851 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3089 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms 341
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling