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The Crystal Structure of Human Neuropeptide Y Y2 Receptor with JNJ-31020028
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ZBQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 293.15 0.1 M HEPES, pH 7.0-7.5, 250-350 mM (NH4)2SO4, and 20-30% PEG500DME, or 0.1 M MES, pH 6.0-6.5, 380-420 mM NH4 tartrate, and 24-26% PEG500DME
Crystal Properties Matthews coefficient Solvent content 4.66 73.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.42 α = 90 b = 50.863 β = 90.667 c = 184.629 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 80 PIXEL DECTRIS PILATUS3 S 6M 2018-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 50 98.4 0.112 12.1 5.4 21815 63.08
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 0.517
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5ZBQ 2.8 37.74 1.36 21815 2020 96.66 0.2581 0.2548 0.2559 0.2891 0.2919 71.06
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 23.1659 f_angle_d 1.2118 f_chiral_restr 0.0605 f_bond_d 0.0108 f_plane_restr 0.0063
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3414 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 73
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing