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Crystal structure of the kainate receptor GluK1 ligand-binding domain in complex with kainate in the absence of glycerol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C32 PDB ENTRY 3C32
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 280 20% PEG4000, 0.35M lithium sulfate, 0.1M sodium cacodylate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Crystal Properties Matthews coefficient Solvent content 2.35 47.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.256 α = 90 b = 68.256 β = 90 c = 235.095 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD MARMOSAIC 225 mm CCD 2011-04-15 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 29.513 100 0.072 9.2 6.4 38773 38773
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 2.11 100 0.411 0.411 1.8 6.4 5508
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 PDB ENTRY 3C32 2 29.513 1.4 38661 1938 99.96 0.1769 0.1747 0.1715 0.2186 0.2142 RANDOM 25.8507
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] 3.3598 3.3598 -6.7196
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.96 f_angle_d 1.004 f_chiral_restr 0.073 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4020 Nucleic Acid Atoms Solvent Atoms 454 Heterogen Atoms 63
Software Software Software Name Purpose SCALA data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing