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Crystal structure of the human glutamate receptor, GluR5, ligand-binding core in complex with 8-deoxy-neodysiherbaine A in space group P1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FVN PDB ENTRY 3FVN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 303 35% PEG3350, 0.3M LiSO4, 5mM 8-deoxy-neodysiherbaine, pH5.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Crystal Properties Matthews coefficient Solvent content 2.26 45.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.508 α = 80.43 b = 50.787 β = 84.41 c = 62.644 γ = 62.1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 IMAGE PLATE MAR scanner 345 mm plate 2008-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 0.9 SPring-8 BL26B2
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 0.036 35.9 3.8 78332
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 87.4 0.261 3.2 3.2 7117
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 3FVN 1.5 30 74370 3918 95.86 0.16727 0.16594 0.1835 0.19148 0.2048 RANDOM 18.303
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] -0.22 0.15 -0.01 -0.54 0.14 0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.101 r_dihedral_angle_3_deg 13.129 r_dihedral_angle_4_deg 12.829 r_dihedral_angle_1_deg 5.476 r_scangle_it 2.777 r_scbond_it 1.85 r_angle_refined_deg 1.242 r_mcangle_it 1.188 r_mcbond_it 0.781 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.101 r_dihedral_angle_3_deg 13.129 r_dihedral_angle_4_deg 12.829 r_dihedral_angle_1_deg 5.476 r_scangle_it 2.777 r_scbond_it 1.85 r_angle_refined_deg 1.242 r_mcangle_it 1.188 r_mcbond_it 0.781 r_nbtor_refined 0.308 r_nbd_refined 0.196 r_symmetry_vdw_refined 0.181 r_symmetry_hbond_refined 0.124 r_xyhbond_nbd_refined 0.11 r_chiral_restr 0.088 r_bond_refined_d 0.009 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 4035 Nucleic Acid Atoms Solvent Atoms 371 Heterogen Atoms 101
Software Software Software Name Purpose MAR345dtb data collection CNS refinement REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing