☰ Navigation Tabs
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 2.46 50.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.751 α = 90 b = 164.541 β = 90 c = 47.46 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 CCD ADSC QUANTUM 210 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.00 APS 17-ID
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 1.5 94.072 98.3 0.071 14.7 6.1 141715 -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 1.5 1.55 87.8 0.305 3.1 12503
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 1.5 94.07 141629 7111 98.13 0.1708 0.169 0.1772 0.203 0.2097 RANDOM 20.4257
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] 0.11 0.08 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.609 r_dihedral_angle_4_deg 20.099 r_dihedral_angle_3_deg 13.313 r_dihedral_angle_1_deg 6.303 r_scangle_it 5.855 r_scbond_it 4.123 r_mcangle_it 2.811 r_angle_refined_deg 2.676 r_mcbond_it 2.233 r_angle_other_deg 1.231
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.609 r_dihedral_angle_4_deg 20.099 r_dihedral_angle_3_deg 13.313 r_dihedral_angle_1_deg 6.303 r_scangle_it 5.855 r_scbond_it 4.123 r_mcangle_it 2.811 r_angle_refined_deg 2.676 r_mcbond_it 2.233 r_angle_other_deg 1.231 r_mcbond_other 0.576 r_xyhbond_nbd_other 0.323 r_nbd_refined 0.283 r_metal_ion_refined 0.258 r_symmetry_vdw_refined 0.251 r_nbd_other 0.215 r_xyhbond_nbd_refined 0.211 r_symmetry_vdw_other 0.205 r_nbtor_refined 0.189 r_symmetry_hbond_refined 0.189 r_chiral_restr 0.17 r_nbtor_other 0.097 r_symmetry_metal_ion_refined 0.056 r_bond_refined_d 0.035 r_gen_planes_refined 0.013 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 1263 Heterogen Atoms 83
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction