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Crystal structure of the iGluR2 ligand-binding core (S1S2J-N754S) in complex with glutamate and NS5217 at 1.50 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FTJ PDB entry 1FTJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 279 20 % PEG 4000, 0.1 M Ammonium sulfate, 0.1 M Cacodylate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Crystal Properties Matthews coefficient Solvent content 2.25 45.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.01 α = 90 b = 47.179 β = 91.88 c = 118.412 γ = 90
Symmetry Space Group P 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MAR CCD 165 mm 2006-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8080 EMBL/DESY, HAMBURG X13
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.49 17.38 85.6 0.041 0.041 25.2 3.7 72325 18
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.49 1.55 95.4 0.405 0.405 2.6 8047
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-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 1FTJ 1.49 17.38 71603 1392 84.51 0.189 0.1941 0.232 0.2368 RANDOM 19.9
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] 0.76 0.84 -1.33 0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.659 r_dihedral_angle_4_deg 21.63 r_dihedral_angle_3_deg 13.571 r_dihedral_angle_1_deg 5.768 r_sphericity_free 4.937 r_scangle_it 2.987 r_scbond_it 2.235 r_sphericity_bonded 2.065 r_mcangle_it 1.44 r_angle_refined_deg 1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.659 r_dihedral_angle_4_deg 21.63 r_dihedral_angle_3_deg 13.571 r_dihedral_angle_1_deg 5.768 r_sphericity_free 4.937 r_scangle_it 2.987 r_scbond_it 2.235 r_sphericity_bonded 2.065 r_mcangle_it 1.44 r_angle_refined_deg 1.36 r_mcbond_it 1.202 r_rigid_bond_restr 1.153 r_angle_other_deg 0.872 r_mcbond_other 0.39 r_nbd_refined 0.213 r_nbd_other 0.19 r_nbtor_refined 0.182 r_symmetry_vdw_other 0.182 r_symmetry_hbond_refined 0.151 r_xyhbond_nbd_refined 0.131 r_symmetry_vdw_refined 0.125 r_nbtor_other 0.09 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4081 Nucleic Acid Atoms Solvent Atoms 683 Heterogen Atoms 96
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection