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Crystal structure of the ATP-gated P2X7 ion channel bound to ATP and allosteric antagonist A804598
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5U1U A804598 bound P2X7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 33% PEG 400, 100 mM MES (pH 6.5), 100 mM NaCl, 5% Glycerol, and 1 mM A804598
Crystal Properties Matthews coefficient Solvent content 5.06 75.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.618 α = 90 b = 167.618 β = 90 c = 167.618 γ = 90
Symmetry Space Group P 21 3
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 PILATUS 6M-F 2016-08-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9791 APS 24-ID-C
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 3.9 48.39 99.9 0.115 0.122 0.039 1 15.4 10 14545 157.97
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.9 4.36 99.9 1.062 0.877 10.3
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 A804598 bound P2X7 3.903 48.387 1.34 14511 1444 99.86 0.3372 0.334 0.3304 0.3856 0.3778
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 8.418 f_angle_d 0.484 f_chiral_restr 0.041 f_plane_restr 0.002 f_bond_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3967 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 149
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction XSCALE data scaling