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Crystal structures of human PYY and NPY
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other generic Fab
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Protein complex (~4 mg/mL with respect to Fab, NPY:Fab at molar ratio of 1.4:1, all dissolved in 25 mM Tris (pH 7.5), 100 mM NaCl) was combined to an equal volume (2 uL) of well solution comprising 200 mM Li2SO4, 100 mM sodium acetate (pH 4.5), 22% (w/v) PEG1000
Crystal Properties Matthews coefficient Solvent content 2.93 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.83 α = 90 b = 136.83 β = 90 c = 116.985 γ = 120
Symmetry Space Group P 62 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2019-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.6 44.79 99.9 0.144 0.15 0.043 0.998 13 12.2 20402
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.72 99.5 1.451 1.512 0.42 0.72 12.7
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 generic Fab 2.6 44.79 19349 1024 99.87 0.2198 0.2171 0.2212 0.2704 0.2689 RANDOM 59.707
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] 0.05 0.03 0.05 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.656 r_dihedral_angle_4_deg 21.863 r_dihedral_angle_3_deg 17.445 r_dihedral_angle_1_deg 8.289 r_angle_refined_deg 1.555 r_angle_other_deg 1.24 r_chiral_restr 0.057 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.656 r_dihedral_angle_4_deg 21.863 r_dihedral_angle_3_deg 17.445 r_dihedral_angle_1_deg 8.289 r_angle_refined_deg 1.555 r_angle_other_deg 1.24 r_chiral_restr 0.057 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3258 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 21
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction