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Crystal structure of the kainate receptor GluK3 ligand binding domain in complex with (S)-1-[2-Amino-2-carboxyethyl]-5,7-dihydrothieno[3,4-d]pyrimidin-2,4(1H,3H)-dione at resolution 2.6A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MH5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.2 279 1.8M sodium/potassium phosphate pH 8.2
Crystal Properties Matthews coefficient Solvent content 2.52 51.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.04 α = 90 b = 68.04 β = 90 c = 126.86 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 2011-06-24 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) Rrim I (All) Rpim I (All) 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 2.6 35.915 99.8 0.108 0.116 0.041 13.5 7.7 9697 33.71
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 2.6 2.74 100 0.433 0.433 0.463 0.16 1.8 7.8
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 THROUGHOUT 4MH5 2.6 35.915 1.41 9695 467 99.66 0.1947 0.1921 0.1913 0.2481 0.2456 47.0813
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 7.939 f_angle_d 0.922 f_chiral_restr 0.052 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2019 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms 22
Software Software Software Name Purpose SCALA data scaling PHENIX refinement PDB_EXTRACT data extraction iMOSFLM data reduction PHASER phasing