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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, dysiherbaine
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 = 118.851 α = 90 b = 65.137 β = 107.03 c = 50.059 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 1.6 50 96.2 0.044 36.9 3.7 46169
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) 1.6 1.66 76.9 0.239 2.27 3.1 3692
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 1.6 30 43859 2307 96.01 0.20029 0.19895 0.1943 0.22538 0.2216 RANDOM 27.956
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] 0.25 -0.64 0.96 -1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.382 r_dihedral_angle_4_deg 15.563 r_dihedral_angle_3_deg 13.301 r_dihedral_angle_1_deg 11.133 r_scangle_it 2.668 r_scbond_it 1.77 r_angle_refined_deg 1.337 r_mcangle_it 1.215 r_mcbond_it 0.81 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.382 r_dihedral_angle_4_deg 15.563 r_dihedral_angle_3_deg 13.301 r_dihedral_angle_1_deg 11.133 r_scangle_it 2.668 r_scbond_it 1.77 r_angle_refined_deg 1.337 r_mcangle_it 1.215 r_mcbond_it 0.81 r_nbtor_refined 0.306 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.186 r_symmetry_hbond_refined 0.116 r_xyhbond_nbd_refined 0.109 r_chiral_restr 0.097 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2131 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing