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Crystal structure of the ATP-gated P2X7 ion channel in the closed, apo state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5U1U A740003 bound P2X7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 100 mM HEPES (pH 7.0), 100 mM NaCl, 4% ethylene glycol, 15% glycerol, 29% PEG-400, 0.1 mg/mL lipid mixture (60% POPE, 20% POPG, and 20% cholesterol).
Crystal Properties Matthews coefficient Solvent content 5.6 78.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.058 α = 90 b = 169.058 β = 90 c = 169.058 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 PIXEL DECTRIS PILATUS3 S 6M 2015-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 1.1051 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 3.4 48.8 99.9 0.099 0.105 0.033 1 16.9 9.8 11207 130.9
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 3.4 3.67 99.8 1.392 1.469 0.462 0.742 10 2280
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 A740003 bound P2X7 3.4 45.183 1.34 11194 1182 99.82 0.2431 0.2406 0.245 0.263 0.2626 125.3547
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 10.115 f_angle_d 0.484 f_chiral_restr 0.042 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2276 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 56
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction XSCALE data scaling PHASER phasing