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Crystal structure of the kainate receptor GluR5 ligand-binding core in complex with (S)-glutamate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FTJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 279 PEG4000, phosphat-citrate buffer, lithiumsulphate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Crystal Properties Matthews coefficient Solvent content 2.24 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.714 α = 90 b = 57.901 β = 102.51 c = 88.75 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD MARRESEARCH 2004-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8128 EMBL/DESY, HAMBURG X11
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 1.94 25 99.7 0.05 18.5 3.1 37489 37372 -3 3 26.9
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) 1.94 2.01 100 0.314 3.9 3721
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 (All) 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 1FTJ 1.95 20.3 35600 1875 99.46 0.20295 0.20295 0.19941 0.2009 0.26885 0.2657 RANDOM 29.497
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] 1.11 -0.95 -0.59 -0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.676 r_dihedral_angle_3_deg 17.347 r_dihedral_angle_4_deg 16.866 r_dihedral_angle_1_deg 7.116 r_scangle_it 4.314 r_scbond_it 2.955 r_mcangle_it 1.994 r_angle_refined_deg 1.876 r_mcbond_it 1.312 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.676 r_dihedral_angle_3_deg 17.347 r_dihedral_angle_4_deg 16.866 r_dihedral_angle_1_deg 7.116 r_scangle_it 4.314 r_scbond_it 2.955 r_mcangle_it 1.994 r_angle_refined_deg 1.876 r_mcbond_it 1.312 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.255 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.196 r_symmetry_hbond_refined 0.159 r_chiral_restr 0.142 r_bond_refined_d 0.021 r_gen_planes_refined 0.008 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 4038 Nucleic Acid Atoms Solvent Atoms 398 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing