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Crystal structure of the ligand-binding core of the human ionotropic glutamate receptor, GluR5, in complex with a novel selective agonist, neodysiherbaine A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZNS PDB ENTRY 2ZNS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 279 PEG3350, NaCl, EDTA, pH4.8, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Crystal Properties Matthews coefficient Solvent content 3.18 61.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.886 α = 90 b = 64.99 β = 107.29 c = 50.232 γ = 90
Symmetry Space Group C 1 2 1
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 270 2007-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.0 Photon Factory BL-17A
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 1.8 50 99.3 0.056 27.6 3.7 33702
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 1.86 96.3 0.294 1.87 2.9 3245
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 2ZNS 1.8 30 32025 1674 99.24 0.19367 0.19142 0.1885 0.23708 0.2352 RANDOM 30.816
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] 0.31 -0.4 1.12 -1.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.91 r_dihedral_angle_4_deg 13.865 r_dihedral_angle_3_deg 13.43 r_dihedral_angle_1_deg 5.906 r_scangle_it 3.131 r_scbond_it 2.034 r_mcangle_it 1.406 r_angle_refined_deg 1.372 r_mcbond_it 0.921 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.91 r_dihedral_angle_4_deg 13.865 r_dihedral_angle_3_deg 13.43 r_dihedral_angle_1_deg 5.906 r_scangle_it 3.131 r_scbond_it 2.034 r_mcangle_it 1.406 r_angle_refined_deg 1.372 r_mcbond_it 0.921 r_nbtor_refined 0.305 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.183 r_xyhbond_nbd_refined 0.147 r_symmetry_hbond_refined 0.119 r_chiral_restr 0.104 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2067 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing