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Crystal structure of the human glutamate receptor, GluR5, ligand-binding core in complex with 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 neodysiherbaine A, pH5.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Crystal Properties Matthews coefficient Solvent content 2.28 46.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.579 α = 85.72 b = 50.712 β = 95.79 c = 63.144 γ = 62.08
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 0.042 32.2 3.8 79267 79267
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 0.157 6.2 3.8 7731
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 75263 3999 96.73 0.1714 0.17016 0.1815 0.19456 0.2018 RANDOM 9.024
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] -0.23 0.22 -0.04 -0.32 -0.01 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.4 r_dihedral_angle_3_deg 12.649 r_dihedral_angle_4_deg 11.196 r_dihedral_angle_1_deg 5.692 r_scangle_it 2.558 r_scbond_it 1.74 r_angle_refined_deg 1.251 r_mcangle_it 1.052 r_mcbond_it 0.737 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.4 r_dihedral_angle_3_deg 12.649 r_dihedral_angle_4_deg 11.196 r_dihedral_angle_1_deg 5.692 r_scangle_it 2.558 r_scbond_it 1.74 r_angle_refined_deg 1.251 r_mcangle_it 1.052 r_mcbond_it 0.737 r_nbtor_refined 0.307 r_nbd_refined 0.193 r_symmetry_vdw_refined 0.172 r_symmetry_hbond_refined 0.119 r_xyhbond_nbd_refined 0.112 r_chiral_restr 0.087 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 4133 Nucleic Acid Atoms Solvent Atoms 471 Heterogen Atoms 115
Software Software Software Name Purpose CNS refinement REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing