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Crystal structure of the kainate receptor GluK3 ligand binding domain in complex with kainate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3S9E PDB ENTRY 3S9E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.2 293 1.8 M SODIUM/POTASSIUM PHOSPHATE, CRYSTALS GROWN IN PRESENCE OF GLUTAMATE SOAKED WITH KAINATE, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.56 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.558 α = 90 b = 68.558 β = 90 c = 126.883 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 2011-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2
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 2.35 48.478 100 0.075 9.7 7.9 13287 13274 36.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.48 100 0.393 0.393 2 8.2
Refinement Statistics Diffraction ID Structure Solution 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 PDB ENTRY 3S9E 2.3501 48.478 1.38 13243 655 99.98 0.1816 0.179 0.1822 0.2322 0.2283 41.9
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] -0.8275 -0.8275 1.655
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.389 f_angle_d 1.062 f_chiral_restr 0.072 f_bond_d 0.012 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2019 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 19
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction XDS data reduction