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Crystal structure of the human glutamate receptor, GluR5, ligand-binding core in complex with 9-deoxy-neodysiherbaine A in space group P1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZNT PDB ENATRY 2ZNT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 303 35% PEG3350, 0.3M LiSO4, 5mM 9-deoxy-neodysiherbaine, pH5.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Crystal Properties Matthews coefficient Solvent content 2.28 46.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.55 α = 80.38 b = 50.814 β = 84.37 c = 63.037 γ = 62.09
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 95.4 0.041 26 2.9 77805
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 1.5 1.55 92 0.212 2.7 2.7 7485
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 ENATRY 2ZNT 1.5 30 73871 3928 95.12 0.17251 0.17159 0.1845 0.18966 0.2001 RANDOM 11.05
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] -0.07 0.08 0.04 -0.24 -0.09 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.379 r_dihedral_angle_3_deg 12.892 r_dihedral_angle_4_deg 10.233 r_dihedral_angle_1_deg 5.549 r_scangle_it 2.491 r_scbond_it 1.714 r_angle_refined_deg 1.287 r_mcangle_it 1.087 r_mcbond_it 0.733 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.379 r_dihedral_angle_3_deg 12.892 r_dihedral_angle_4_deg 10.233 r_dihedral_angle_1_deg 5.549 r_scangle_it 2.491 r_scbond_it 1.714 r_angle_refined_deg 1.287 r_mcangle_it 1.087 r_mcbond_it 0.733 r_nbtor_refined 0.309 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.174 r_symmetry_hbond_refined 0.118 r_xyhbond_nbd_refined 0.101 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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 4012 Nucleic Acid Atoms Solvent Atoms 448 Heterogen Atoms 101
Software Software Software Name Purpose CNS refinement REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing