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Crystal Structure of the human glutamate receptor, GluR5, ligand-binding core in complex with dysiherbaine 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 dysiherbaine, pH5.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Crystal Properties Matthews coefficient Solvent content 2.28 46.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.486 α = 80.08 b = 50.74 β = 84.18 c = 63.252 γ = 62.06
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 97 0.049 29.6 3.8 79411
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 0.193 3.8 3.7 7741
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 75397 4011 96.82 0.17154 0.1706 0.1842 0.18895 0.1996 RANDOM 12.771
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] -0.11 0.16 -0.02 -0.25 -0.04 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.695 r_dihedral_angle_3_deg 12.71 r_dihedral_angle_4_deg 9.997 r_dihedral_angle_1_deg 5.563 r_scangle_it 2.682 r_scbond_it 1.767 r_angle_refined_deg 1.27 r_mcangle_it 1.08 r_mcbond_it 0.924 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.695 r_dihedral_angle_3_deg 12.71 r_dihedral_angle_4_deg 9.997 r_dihedral_angle_1_deg 5.563 r_scangle_it 2.682 r_scbond_it 1.767 r_angle_refined_deg 1.27 r_mcangle_it 1.08 r_mcbond_it 0.924 r_nbtor_refined 0.309 r_nbd_refined 0.195 r_symmetry_vdw_refined 0.161 r_symmetry_hbond_refined 0.124 r_xyhbond_nbd_refined 0.115 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4154 Nucleic Acid Atoms Solvent Atoms 462 Heterogen Atoms 85
Software Software Software Name Purpose CNS refinement REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing