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Crystal structure of the kainate receptor GluK3 ligand-binding domain in complex with the agonist ZA302
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3S9E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.2 280 1.8M sodium/potassium phosphate, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Crystal Properties Matthews coefficient Solvent content 2.53 51.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.18 α = 90 b = 68.18 β = 90 c = 126.52 γ = 90
Symmetry Space Group P 41 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 CCD MARMOSAIC 225 mm CCD 2012-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 1.0000 MAX II I911-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.65 42.173 98.7 0.108 9.5 4.6 9062 49
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.79 99.9 0.39 0.39 0.442 0.201 1.9 4.6 1307
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3S9E 2.65 35.866 1.36 9029 432 97.9 0.2014 0.198 0.1957 0.2671 0.2656 RANDOM 49.3494
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] -0.3157 -0.3157 0.6314
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.342 f_angle_d 1.166 f_chiral_restr 0.074 f_bond_d 0.017 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2011 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 25
Software Software Software Name Purpose SCALA data scaling PHENIX refinement PDB_EXTRACT data extraction MOSFLM data reduction PHASER phasing