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Crystal structure of the ATP-gated P2X7 ion channel bound to allosteric antagonist A740003
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DW0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 100 mM HEPES or Tris (pH 6.0-7.5), 100 mM NaCl, 4% ethylene glycol, 15% glycerol, 27-32% PEG-400 or 31-36% PEG-300, 0.1 mg/mL lipid mixture (60% POPE, 20% POPG, and 20% cholesterol), and 1 mM A740003
Crystal Properties Matthews coefficient Solvent content 5.24 76.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.566 α = 90 b = 169.566 β = 90 c = 169.566 γ = 90
Symmetry Space Group I 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 CCD ADSC QUANTUM 315 2015-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.9792 APS 24-ID-E
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 3.6 45.32 99.9 0.228 0.239 0.072 0.996 13 11 9537 106.64
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 3.6 3.95 99.9 1.243 0.752 11.1
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 4DW0 3.604 45.318 1.33 9512 1027 99.66 0.236 0.233 0.2344 0.2608 0.2573 97.841
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 12.111 f_angle_d 0.661 f_chiral_restr 0.046 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2307 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 77
Software Software Software Name Purpose Aimless data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction XSCALE data scaling