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Crystal structure of the human glutamate receptor, GluR5, ligand-binding core in complex with L-glutamate 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, pH5.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Crystal Properties Matthews coefficient Solvent content 2.29 46.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.617 α = 93.52 b = 50.724 β = 96.41 c = 63.254 γ = 117.86
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 ADSC QUANTUM 270 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 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 1.65 50 96.3 0.074 19 3.9 59662 59662
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) 1.65 1.71 91.3 0.378 2 3.6 5634
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 1.65 30 56612 3010 96.14 0.19023 0.18866 0.1961 0.21936 0.22 RANDOM 13.107
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] -0.45 -0.19 0.17 -0.57 0.06 0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.054 r_dihedral_angle_3_deg 13.249 r_dihedral_angle_4_deg 12.944 r_dihedral_angle_1_deg 5.729 r_scangle_it 3.232 r_scbond_it 2.141 r_angle_refined_deg 1.313 r_mcangle_it 1.24 r_mcbond_it 0.84 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.054 r_dihedral_angle_3_deg 13.249 r_dihedral_angle_4_deg 12.944 r_dihedral_angle_1_deg 5.729 r_scangle_it 3.232 r_scbond_it 2.141 r_angle_refined_deg 1.313 r_mcangle_it 1.24 r_mcbond_it 0.84 r_nbtor_refined 0.307 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.183 r_xyhbond_nbd_refined 0.121 r_symmetry_hbond_refined 0.115 r_chiral_restr 0.093 r_bond_refined_d 0.012 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 4082 Nucleic Acid Atoms Solvent Atoms 436 Heterogen Atoms 35
Software Software Software Name Purpose HKL-2000 data collection CNS refinement REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing