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Crystal structure of the human glutamate receptor, GluR5, ligand-binding core in complex with 8-epi-neodysiherbaine A in space group P1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZNT PDB ENTRY 2ZNT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 303 35% PEG3350, 0.3M LiSO4, 5mM 8-epi-neodysiherbaine, pH5.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Crystal Properties Matthews coefficient Solvent content 2.29 46.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.717 α = 94.19 b = 50.756 β = 95.9 c = 63.29 γ = 117.95
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD RIGAKU JUPITER 210 2008-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 0.9 SPring-8 BL26B1
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 1.5 50 96.9 0.05 29.3 3.6 79930
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) 1.5 1.55 95.1 0.135 5.11 3.5 7800
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 2ZNT 1.5 30 75913 4013 96.79 0.16619 0.16485 0.1819 0.19119 0.2007 RANDOM 7.926
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] 0.01 0.08 -0.12 0.05 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.082 r_dihedral_angle_3_deg 12.758 r_dihedral_angle_4_deg 10.667 r_dihedral_angle_1_deg 5.425 r_scangle_it 2.499 r_scbond_it 1.682 r_angle_refined_deg 1.255 r_mcangle_it 1.06 r_mcbond_it 0.711 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.082 r_dihedral_angle_3_deg 12.758 r_dihedral_angle_4_deg 10.667 r_dihedral_angle_1_deg 5.425 r_scangle_it 2.499 r_scbond_it 1.682 r_angle_refined_deg 1.255 r_mcangle_it 1.06 r_mcbond_it 0.711 r_nbtor_refined 0.308 r_nbd_refined 0.197 r_symmetry_vdw_refined 0.168 r_xyhbond_nbd_refined 0.111 r_symmetry_hbond_refined 0.101 r_chiral_restr 0.083 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4197 Nucleic Acid Atoms Solvent Atoms 510 Heterogen Atoms 128
Software Software Software Name Purpose CNS refinement REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing