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Crystal structures of GLuR2 ligand-binding-domain in complex with glutamate and positive allosteric modulators
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LBC PDB ENTRY 1LBC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 1 uL 7 mg/mL protein in 10 mM (S)-Glu, 10 mM HEPES, pH 7.5, 20 mM sodium chloride, 1 mM EDTA, 150 uM ligand (from 30 mM DMSO stock) + 1 uL reservoir (10% PEG8000, 0.1 M zinc acetate, 0.1 M sodium acetate, pH 5.5), crystals appeared in 3-5 days, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.45 49.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.676 α = 90 b = 164.953 β = 90 c = 47.498 γ = 90
Symmetry Space Group P 21 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 100 IMAGE PLATE RIGAKU RAXIS HTC mirrors M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E DW 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.85 93.659 96.9 0.06 15.3 6.4 74948 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.92 94.3 5.6 7181
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1LBC 1.85 93.659 74877 3834 96.85 0.1982 0.1963 0.2316 0.2181 RANDOM 20.2948
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] -0.02 0.35 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.012 r_dihedral_angle_4_deg 19.954 r_dihedral_angle_3_deg 15.15 r_dihedral_angle_1_deg 6.295 r_scangle_it 4.429 r_scbond_it 2.923 r_angle_refined_deg 1.861 r_mcangle_it 1.815 r_mcbond_it 1.058 r_angle_other_deg 1.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.012 r_dihedral_angle_4_deg 19.954 r_dihedral_angle_3_deg 15.15 r_dihedral_angle_1_deg 6.295 r_scangle_it 4.429 r_scbond_it 2.923 r_angle_refined_deg 1.861 r_mcangle_it 1.815 r_mcbond_it 1.058 r_angle_other_deg 1.016 r_mcbond_other 0.358 r_chiral_restr 0.115 r_bond_refined_d 0.023 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6035 Nucleic Acid Atoms Solvent Atoms 346 Heterogen Atoms 93
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction AMoRE phasing