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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 49.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.38 α = 90 b = 164.344 β = 90 c = 47.402 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 IV++ mirrors M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 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 2.1 30 100 0.142 6.3 7.2 53393 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.18 100 0.719 7.1 5281
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1LBC 2.1 30 53166 2674 99.97 0.1978 0.1955 0.1967 0.2396 0.2399 RANDOM 17.1859
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] 0.09 0.02 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.848 r_dihedral_angle_4_deg 19.424 r_dihedral_angle_3_deg 15.814 r_dihedral_angle_1_deg 6.372 r_scangle_it 3.385 r_scbond_it 2.281 r_angle_refined_deg 1.647 r_mcangle_it 1.387 r_mcbond_it 1.013 r_angle_other_deg 1.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.848 r_dihedral_angle_4_deg 19.424 r_dihedral_angle_3_deg 15.814 r_dihedral_angle_1_deg 6.372 r_scangle_it 3.385 r_scbond_it 2.281 r_angle_refined_deg 1.647 r_mcangle_it 1.387 r_mcbond_it 1.013 r_angle_other_deg 1.004 r_mcbond_other 0.248 r_nbd_refined 0.246 r_symmetry_vdw_refined 0.244 r_symmetry_vdw_other 0.223 r_nbd_other 0.2 r_nbtor_refined 0.18 r_symmetry_hbond_refined 0.147 r_xyhbond_nbd_refined 0.138 r_metal_ion_refined 0.112 r_chiral_restr 0.093 r_nbtor_other 0.09 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6035 Nucleic Acid Atoms Solvent Atoms 251 Heterogen Atoms 79
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction AMoRE phasing