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X-ray structure of iGluR5 ligand-binding core (S1S2) in complex with dysiherbaine at 1.35A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YCJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 280 PEG8000, ammonium sulfate, phosphate-citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Crystal Properties Matthews coefficient Solvent content 2.28 45.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.872 α = 92.69 b = 66.902 β = 94.66 c = 90.342 γ = 100.82
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 MAR CCD 165 mm 2006-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 1.000 MAX II I911-2
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 1.35 89.862 94.8 0.079 0.079 5.073 3.6 213789 213789 9.964
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 1.35 1.42 90.2 0.342 0.342 1.7 3.6 29699
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1ycj 1.35 89.8 213779 209482 4297 94.8 0.165 0.165 0.193 0.2159 RANDOM 10.008
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] -0.09 -0.01 0.02 0.02 0.03 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.123 r_dihedral_angle_3_deg 10.855 r_dihedral_angle_4_deg 9.819 r_dihedral_angle_1_deg 5.589 r_sphericity_free 3.365 r_scangle_it 2.796 r_sphericity_bonded 2.112 r_scbond_it 2.086 r_mcangle_it 1.369 r_mcbond_it 1.217
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.123 r_dihedral_angle_3_deg 10.855 r_dihedral_angle_4_deg 9.819 r_dihedral_angle_1_deg 5.589 r_sphericity_free 3.365 r_scangle_it 2.796 r_sphericity_bonded 2.112 r_scbond_it 2.086 r_mcangle_it 1.369 r_mcbond_it 1.217 r_angle_refined_deg 1.174 r_rigid_bond_restr 1.087 r_angle_other_deg 0.817 r_mcbond_other 0.373 r_symmetry_vdw_other 0.231 r_nbd_refined 0.207 r_nbd_other 0.182 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.11 r_symmetry_hbond_refined 0.1 r_nbtor_other 0.086 r_symmetry_vdw_refined 0.082 r_chiral_restr 0.072 r_xyhbond_nbd_other 0.027 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8069 Nucleic Acid Atoms Solvent Atoms 1441 Heterogen Atoms 114
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection